5IV5

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.11 Å
  • Aggregation State: Particle
  • Reconstruction Method: Single Particle

Literature

Macromolecules
Sequence Display for 5IV5

Classification: VIRAL PROTEIN

Total Structure Weight: 6490099.00

Macromolecule Entities
Molecule Chains Length Organism Details
Baseplate wedge protein gp6 A, B, BH..., BI, EA, EB, GD, GE, X, Y, u, vA, B, BH, BI, EA, EB, GD, GE, X, Y, u, v 660 Enterobacteria phage t4 sensu lato Gene Name(s): 6
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Baseplate wedge protein gp7 BJ, C, EC..., GF, Z, wBJ, C, EC, GF, Z, w 1032 Enterobacteria phage t4 sensu lato Gene Name(s): 7
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Baseplate wedge protein gp8 CA, CB, D..., E, ED, EE, GG, GH, a, b, x, yCA, CB, D, E, ED, EE, GG, GH, a, b, x, y 334 Enterobacteria phage t4 sensu lato Gene Name(s): 8
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Baseplate wedge protein gp9 AA, AB, CC..., CD, CE, EF, EG, EH, F, G, GI, GJ, H, HA, c, d, e, zAA, AB, CC, CD, CE, EF, EG, EH, F, G, GI, GJ, H, HA, c, d, e, z 288 Enterobacteria phage t4 sensu lato Gene Name(s): 9
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Baseplate wedge protein gp10 AC, AD, AE..., CF, CG, CH, EI, EJ, FA, HB, HC, HD, I, J, K, f, g, hAC, AD, AE, CF, CG, CH, EI, EJ, FA, HB, HC, HD, I, J, K, f, g, h 602 Enterobacteria phage t4 sensu lato Gene Name(s): 10
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Baseplate wedge protein gp11 AF, AG, AH..., CI, CJ, DA, FB, FC, FD, HE, HF, HG, L, M, N, i, j, kAF, AG, AH, CI, CJ, DA, FB, FC, FD, HE, HF, HG, L, M, N, i, j, k 219 Enterobacteria phage t4 sensu lato Gene Name(s): 11
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Short tail fiber protein gp12 AI, AJ, BA..., DB, DC, DD, FE, FF, FG, HH, HI, HJ, O, P, Q, l, m, nAI, AJ, BA, DB, DC, DD, FE, FF, FG, HH, HI, HJ, O, P, Q, l, m, n 527 Enterobacteria phage t4 sensu lato Gene Name(s): 12
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Tail tube protein gp19 BB, BC, DE..., DF, FH, FI, IA, IB, R, S, o, pBB, BC, DE, DF, FH, FI, IA, IB, R, S, o, p 163 Enterobacteria phage t4 sensu lato Gene Name(s): 19
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Baseplate wedge protein gp25 BD, DG, FJ..., IC, T, qBD, DG, FJ, IC, T, q 132 Enterobacteria phage t4 sensu lato Gene Name(s): 25
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Baseplate tail-tube protein gp48 BE, DH, GA..., ID, U, rBE, DH, GA, ID, U, r 364 Enterobacteria phage t4 sensu lato Gene Name(s): 48
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Baseplate wedge protein gp53 BF, DI, GB..., IE, V, sBF, DI, GB, IE, V, s 196 Enterobacteria phage t4 sensu lato Gene Name(s): 53
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Baseplate tail-tube protein gp54 BG, DJ, GC..., IF, W, tBG, DJ, GC, IF, W, t 320 Enterobacteria phage t4 sensu lato Gene Name(s): 54
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Peptidoglycan hydrolase gp5 YA, YB, YC 575 Enterobacteria phage t4 sensu lato EC#: 3.2.1.17 IUBMB
Details: The chain breaks in gp5 (chains YA, YB and YC) between residues 76 and 77 were introduced by the refinement program. The starting model did not contain these breaks. This region lies in the symmetry mismatched region of our map and cannot be refined reliably. The crystal structure of the gp5-gp27 complex - PDB code 1K28 - gives a more precise description of the polypeptide chain conformation at this location.
Gene Name(s): 5
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Baseplate hub protein gp27 YD, YE, YF 391 Enterobacteria phage t4 sensu lato Gene Name(s): 27
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Uncharacterized 10.2 kDa protein in segC-Gp6 intergenic region ZA 97 Enterobacteria phage t4 sensu lato Gene Name(s): y08B 5.4
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

AI, DB, FE, HH, O, l ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

ZA FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.11 Å
  • Reconstruction Method: Single Particle

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2016-03-19
  • Released Date: 2016-05-18
  • Deposition author(s): Taylor, N.M.I., Guerrero-Ferreira, R.C., Goldie, K.N., Stahlberg, H., Leiman, P.G.

Revision History

  • Version 1_0: 2016-05-18

    Type: Initial release

  • Version 1_1: 2016-05-25

    Type: Database references

  • Version 1_2: 2016-06-08

    Type: Database references

  • Version 1_3: 2017-08-30

    Type: Advisory, Data collection