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Leiman Research Lab

Structures


Protein Data Bank (PDB)
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5LYE

Re-refined structure of the bacteriophage T4 short tail fibre PDB entry 1H6W containing 71 additionally identified residues

Taylor NMI, van Raaij MJ, Leiman PG.

Contractile injection systems of bacteriophages and related systems. Mol. Microbiol. (2018) [PubMed]

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5IW9

Structure of bacteriophage T4 gp25, sheath polymerization initiator

Taylor NM, Prokhorov NS, Guerrero-Ferreira RC, Shneider MM, Browning C, Goldie KN, Stahlberg H, Leiman PG.

Structure of the T4 baseplate and its function in triggering sheath contraction. Nature 533, 346-52 (2016) [PubMed]


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5CES

C-terminal domain of the R-type pyocin baseplate protein PA0618

Leiman PG, Plattner M, Buth SA, Shneider MM

 

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4Y9V

Gp54 tailspike of Acinetobacter baumannii bacteriophage AP22 in complex with A. baumannii capsular saccharide

Buth SA, Shneider MM, Leiman PG


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4S36

Crystal structure of the C-terminal domain of R2 pyocin membrane-piercing spike

Browning CB, Leiman PG, Shneider MM

 

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4S37

Crystal structure of R2 pyocin membrane-piercing spike

Browning CB, Leiman PG, Shneider MM


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4RMX

Apo crystal structure of the colanidase tailspike protein gp150 of Phage Phi92

Browning C, Schwarzer D, Gerardy-Schahn R, Shneider MM, Leiman PG

 

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4RU3

Crystal structure of the cell puncturing protein gp41 from Pseudomonas phage SN

Browning C, Shneider MM, Leiman PG


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4RU4

Crystal structure of the tailspike protein gp49 from Pseudomonas phage LKA1

Olszak T, Shneider MM, Latka A, Maciejewska B, Browning C, Sycheva LV, Cornelissen A, Danis-Wlodarczyk K, Senchenkova SN, Shashkov AS, Gula G, Arabski M, Wasik S, Miroshnikov KA, Lavigne R, Leiman PG, Knirel YA, Drulis-Kawa Z.

The O-specific polysaccharide lyase from the phage LKA1 tailspike reduces Pseudomonas virulence. Sci Rep 7(1):16302 (2017). [PubMed]

 

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4RU5

Crystal Structure of the Pseudomonas phage phi297 tailspike gp61

Olszak T, Shneider MM, Latka A, Maciejewska B, Browning C, Sycheva LV, Cornelissen A, Danis-Wlodarczyk K, Senchenkova SN, Shashkov AS, Gula G, Arabski M, Wasik S, Miroshnikov KA, Lavigne R, Leiman PG, Knirel YA, Drulis-Kawa Z.

The O-specific polysaccharide lyase from the phage LKA1 tailspike reduces Pseudomonas virulence. Sci Rep 7(1):16302 (2017). [PubMed]


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4OSD

Dimer of a C-terminal fragment of phage T4 gp5 beta-helix

Buth SA, Leiman PG, Shneider MM

 

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4QNL

Crystal structure of tail fiber protein gp63.1 from E. coli phage G7C

Prokhorov NS, Riccio C, Zdorovenko EL, Shneider MM, Browning C, Knirel YA, Leiman PG, Letarov AV

Function of bacteriophage G7C esterase tailspike in host cell adsorption. Mol. Microbiol. 105, 385-398 (2017) [PubMed]


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4MTM

Crystal structure of the tail fiber gp53 from Acinetobacter baumannii bacteriophage AP22

Sycheva LV, Shneider MM, Popova AV, Ziganshin RK, Miroshnikov KA, Leiman, PG

 

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4MTK

Crystal structure of PA0091 VgrG1, the central spike of the Type VI Secretion System

Sycheva LV, Shneider M, Basler M, Ho BT, Mekalanos JJ, Leiman PG


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4KU0

Phage T4 spike tip protein gp5.4 in complex with T4 gp5 beta-helix

Buth SA, Shneider MM, Leiman PG

Gp5.4 amino acid sequence and gene information is here. Gp5 amino acid sequence and gene information is here (residues 484-575).
Gp5 and gp5.4 were co-expressed in cis. Expression construct type: His-tag_TEV-cleavage-site_gp5...gp5.4.
Expression vector: pEEva2 (pET-23a derivate).

 

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4JJ2

Structure and biophysical properties of phage T4 gp5 beta-helix

Buth SA, Leiman PG, Boudko SP


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4HIZ

Catalytic domain of phage phi92 endosialidase (residues 76-756 of gp143)

Schwarzer D, Browning C, Leiman PG

Amino acid sequence and gene information is here

Expression construct type: Strep-tag_Thrombin-cleavage-site_gp143(aa76-918)_His-tag

Expression vector: pET22b-Strep (pET22b with N-terminal Strep-tag)

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3WIT

PAAR-repeat binding tip (residues 561-633) of the Z0707 VgrG protein of E. coli EDL933

Uchida K, Leiman PG, Arisaka F, Kanamaru S

Structure and properties of the C-terminal β-helical domain of VgrG protein from Escherichia coli O157. J. Biochem. 155, 173-182 (2013). [PubMed]

Amino acid sequence and gene information is here

Expression construct type: His-tag_SlyD-TEV-cleavage-site_z0707

Expression vector: pESL (pET28a derivative)


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4HRZ

Phage T4 baseplate protein gp25

Browning C, Shneider MM, Leiman PG

Amino acid sequence is here

Expression construct type: His-tag_SlyD-TEV-cleavage-site_gp25

Expression vector: pESL (pET28a derivative)

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4JIW

c1882 PAAR-repeat protein of E. coli CFT073 in complex with T4 gp5-VgrG chimera

Shneider MM, Buth SA, Ho BT, Basler M, Mekalanos JJ, Leiman PG

PAAR-repeat proteins sharpen and diversify the type VI secretion system spike. Nature. 500, 350-353 (2013). [PubMed]

Gp5 amino acid sequence is here (residues 484-575). Expression construct type: His-tag_TEV-cleavage-site_gp5. Expression vector: pEEva2 (pET-23a derivate).

c1882 amino acid sequence is here. Expression construct type: untagged. Expression vector: pATE (pACYCDuet-1 derivative).


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4JIV

VCA0105 PAAR-repeat protein of V. cholerae O1 biovar El Tor str. N16961 in complex with T4 gp5-VgrG chimera

Shneider MM, Buth SA, Ho BT, Basler M, Mekalanos JJ, Leiman PG

PAAR-repeat proteins sharpen and diversify the type VI secretion system spike. Nature. 500, 350-353 (2013). [PubMed]

Gp5 amino acid sequence is here (residues 484-575). Expression construct type: His-tag_TEV-cleavage-site_gp5. Expression vector: pEEva2 (pET-23a derivate).

VCA0105 amino acid sequence is here. Expression construct type: untagged. Expression vector: pATE (pACYCDuet-1 derivative).

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4JK6

Human urokinase-type plasminogen activator uPA with bound bicyclic peptide inhibitor UK18-D-Aba

Chen S, Gfeller D, Buth SA, Michielin O, Leiman PG, Heinis C

Improving Binding Affinity and Stability of Peptide Ligands by Substituting Glycines with D-Amino Acids. Chembiochem. 14, 1316-1322 (2013). [PubMed]

Amino acid sequence and gene information is here.

Commercially produced protein purchased here.


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4JK5

Human urokinase-type plasminogen activator uPA with bound bicyclic peptide inhibitor UK18-D-Ser

Chen S, Gfeller D, Buth SA, Michielin O, Leiman PG, Heinis C

Improving Binding Affinity and Stability of Peptide Ligands by Substituting Glycines with D-Amino Acids. Chembiochem. 14, 1316-1322 (2013). [PubMed]

Amino acid sequence and gene information is here.

Commercially produced protein purchase here.

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4GLY

Human urokinase-type plasminogen activator uPA with bound bicyclic peptide inhibitor UK504

Chen S, Rentero Rebollo I, Buth SA, Morales-Sanfrutos J, Touati J, Leiman PG, Heinis C

Bicyclic Peptide Ligands Pulled out of Cysteine-Rich Peptide Libraries. J. Am. Chem. Soc. 135, 6562-6569. (2013). [PubMed]

Amino acid sequence and gene information is here.

Commercially produced protein purchased here.


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4GBF

C-terminal fragment of phage phiKZ tail fiber protein gp131 (residues 375-771)

Sycheva LV, Shneider MM, Sykilinda NN, Ivanova MA, Miroshnikov KA, Leiman PG

Crystal structure and location of gp131 in the bacteriophage phiKZ virion. Virology. 434, 257-264 (2012). [PubMed]

Amino acid sequence and gene information is here.

Expression construct type: His-tag_SlyD-TEV-cleavage-site_gp131

Expression vector: pESL (pET28a derivative)

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3PQH

C-terminal fragment of phage phi92 central spike protein gp138 (residues 121-245)

Browning C, Shneider MM, Bowman VD, Schwarzer D, Leiman PG

Phage pierces the host cell membrane with the iron-loaded spike. Structure. 20:326-339 (2012). [PubMed]

Amino acid sequence and gene information is here.

Expression construct type: His-tag_TEV-cleavage-site_gp138C

Expression vector: pEEVa2 (pET-23a derivate


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3PQI

Phage phi92 central spike protein gp138

Browning C, Shneider MM, Bowman VD, Schwarzer D, Leiman PG

Phage pierces the host cell membrane with the iron-loaded spike. Structure. 20:326-339 (2012). [PubMed]

Amino acid sequence and gene information is here.

Expression construct type: His-tag_TEV-cleavage-site_gp138

Expression vector: pEEVa2 (pET-23a derivate)

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3QR7

C-terminal fragment of phage P2 central spike protein gpV (residues 97- 211)

Browning C, Shneider MM, Bowman VD, Schwarzer D, Leiman PG

Phage pierces the host cell membrane with the iron-loaded spike. Structure. 20:326-339 (2012). [PubMed]

Amino acid sequence and gene information is here.

Expression construct type: His-tag_TEV-cleavage-site_gpVC

Expression vector: pEEVa2 (pET-23a derivate)


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3QR8

Phage P2 central spike protein gpV

Browning C, Shneider MM, Bowman VD, Schwarzer D, Leiman PG

Phage pierces the host cell membrane with the iron-loaded spike. Structure. 20:326-339 (2012). [PubMed]

Amino acid sequence and gene information is here.

Expression construct type: His-tag_TEV-cleavage-site_gpV

Expression vector: pEEVa2 (pET-23a derivate)

  

Electron Microscopy Data Bank (EMDB)
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EMD-8767

Cryo-EM structure of the T4 tail tube

Zheng W, Wang F, Taylor NMI, Guerrero-Ferreira RC, Leiman PG, Egelman EH

Refined Cryo-EM Structure of the T4 Tail Tube: Exploring the Lowest Dose Limit. Structure 25, 1436-1441.e2 (2017) [PubMed]

  

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EMD-8396

Asymmetric reconstruction of bacteriophage MS2 mutant NEO1

Zhong Q, Carratala A, Nazarov S, Guerrero-Ferreira RC, Piccinini L, Bachmann V, Leiman PG, Kohn T

Genetic, Structural, and Phenotypic Properties of MS2 Coliphage with Resistance to ClO2 Disinfection. Environ. Sci. Technol. 50, 13520-13528 (2016) [PubMed]

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EMD-8360

Asymmetric reconstruction of bacteriophage MS2

Zhong Q, Carratala A, Nazarov S, Guerrero-Ferreira RC, Piccinini L, Bachmann V, Leiman PG, Kohn T

Genetic, Structural, and Phenotypic Properties of MS2 Coliphage with Resistance to ClO2 Disinfection. Environ. Sci. Technol. 50, 13520-13528 (2016) [PubMed]


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EMD-3374

Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex

Taylor NMI, Prokhorov NS, Guerrero-Ferreira RC, Shneider MM, Browning C, Goldie KN, Stahlberg H, Leiman PG

Structure of bacteriophage T4 baseplate and its function in triggering sheath contraction. NATURE 533, 346-52 (2016) [PubMed]

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EMD-3392

Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex: locally masked refinement of the inner baseplate

Taylor NMI, Prokhorov NS, Guerrero-Ferreira RC, Shneider MM, Browning C, Goldie KN, Stahlberg H, Leiman PG

Structure of bacteriophage T4 baseplate and its function in triggering sheath contraction. NATURE 533, 346-52 (2016) [PubMed]


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EMD-3393

Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex: locally masked refinement of the intermediate baseplate

Taylor NMI, Prokhorov NS, Guerrero-Ferreira RC, Shneider MM, Browning C, Goldie KN, Stahlberg H, Leiman PG

Structure of bacteriophage T4 baseplate and its function in triggering sheath contraction. NATURE 533, 346-52 (2016) [PubMed]

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EMD-3394

Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex: locally masked refinement of the upper peripheral baseplate

Taylor NMI, Prokhorov NS, Guerrero-Ferreira RC, Shneider MM, Browning C, Goldie KN, Stahlberg H, Leiman PG

Structure of bacteriophage T4 baseplate and its function in triggering sheath contraction. NATURE 533, 346-52 (2016) [PubMed]


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EMD-3395

Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex: locally masked refinement of the lower peripheral baseplate

Taylor NMI, Prokhorov NS, Guerrero-Ferreira RC, Shneider MM, Browning C, Goldie KN, Stahlberg H, Leiman PG

Structure of bacteriophage T4 baseplate and its function in triggering sheath contraction. NATURE 533, 346-52 (2016) [PubMed]

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EMD-3396

Cryo-electron microscopy structure of the star-shaped, hubless post-attachment T4 baseplate

Taylor NMI, Prokhorov NS, Guerrero-Ferreira RC, Shneider MM, Browning C, Goldie KN, Stahlberg H, Leiman PG

Structure of bacteriophage T4 baseplate and its function in triggering sheath contraction. NATURE 533, 346-52 (2016) [PubMed]


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EMD-3397

Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex: locally masked refinement of the tail tube

Taylor NMI, Prokhorov NS, Guerrero-Ferreira RC, Shneider MM, Browning C, Goldie KN, Stahlberg H, Leiman PG

Structure of bacteriophage T4 baseplate and its function in triggering sheath contraction. NATURE 533, 346-52 (2016) [PubMed]

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EMD-6271

Atomic structures of a bactericidal contractile nanotube in its pre- and post-contraction states

Ge P, Scholl D, Leiman PG, Yu X, Miller JF, Zhou ZH

Atomic structures of a bactericidal contractile nanotube in its pre- and post-contraction states. NAT.STRUCT.MOL.BIOL. 22, 377-382 (2015) [PubMed]


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EMD-6270

Atomic structures of a bactericidal contractile nanotube in its pre- and post-contraction states

Ge P, Scholl D, Leiman PG, Yu X, Miller JF, Zhou ZH

Atomic structures of a bactericidal contractile nanotube in its pre- and post-contraction states. NAT.STRUCT.MOL.BIOL. 22, 377-382 (2015) [PubMed]

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EMD-5409

Cryo-electron microscopy structure of bacteriophage phi92 tail

Nazarov S, Bowman VD, Leiman PG

Phi92 genome is here.


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EMD-2064

Cryo-electron microscopy structure of bacteriophage phi92 baseplate

Browning C, Nazarov S, Bowman VD, Leiman PG

Phi92 genome is here.

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EMD-2063

Cryo-electron microscopy structure of bacteriophage phi92 capsid

Browning C, Nazarov S, Bowman VD, Leiman PG

Phi92 genome is here.

PDB 4RMY

Colanic acid-bound crystal structure of the colanidase tailspike protein gp150 of Phage Phi92

Browning, C., Schwarzer, D., Gerardy-Schahn, R., Shneider, M.M., Leiman, P.G.