7WMP | pdb_00007wmp

Tail structure of Helicobacter pylori bacteriophage KHP30

PDB DOI: https://doi.org/10.2210/pdb7WMP/pdb
EM Map EMD-32616: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Helicobacter phage KHP30
Mutation(s): No

Deposited: 2022-01-15 Released: 2023-03-01
Deposition Author(s): Kamiya, R., Uchiyama, J., Matsuzaki, S., Murata, K., Iwasaki, K., Miyazaki, N.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 7WMP

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of Helicobacter pylori bacteriophage KHP30

Kamiya, R., Uchiyama, J., Matsuzaki, S., Murata, K., Iwasaki, K., Miyazaki, N.

To be published.

Macromolecule Content

Total Structure Weight: 1,463.83 kDa
Atom Count: 98,184
Modeled Residue Count: 12,204
Deposited Residue Count: 12,744
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Portal protein	A [auth a] B [auth b] C [auth c] D [auth d] E [auth e] A [auth a], B [auth b], C [auth c], D [auth d], E [auth e], F [auth f], G [auth g], H [auth h], I [auth i], J [auth j], K [auth k], L [auth l]	602	Helicobacter phage KHP30	Mutation(s): 0
UniProt
Find proteins for I7HHN4 (Helicobacter pylori bacteriophage KHP30) Explore I7HHN4 Go to UniProtKB: I7HHN4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I7HHN4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Adaptor protein gp12	M [auth m] N [auth n] O [auth o] P [auth p] Q [auth q] M [auth m], N [auth n], O [auth o], P [auth p], Q [auth q], R [auth r], S [auth s], T [auth t], U [auth u], V [auth v], W [auth w], X [auth x]	195	Helicobacter phage KHP30	Mutation(s): 0
UniProt
Find proteins for I7HHN3 (Helicobacter pylori bacteriophage KHP30) Explore I7HHN3 Go to UniProtKB: I7HHN3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I7HHN3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nozzle protein gp25	AA [auth C] BA [auth D] CA [auth E] DA [auth F] EA [auth G] AA [auth C], BA [auth D], CA [auth E], DA [auth F], EA [auth G], FA [auth H], GA [auth I], HA [auth J], IA [auth K], JA [auth L], Y [auth A], Z [auth B]	265	Helicobacter phage KHP30	Mutation(s): 0
UniProt
Find proteins for I7HFX1 (Helicobacter pylori bacteriophage KHP30) Explore I7HFX1 Go to UniProtKB: I7HFX1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I7HFX1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	15K18521
Japan Society for the Promotion of Science (JSPS)	Japan	18K06154

Revision History (Full details and data files)

Version 1.0: 2023-03-01
Type: Initial release
Version 1.1: 2024-06-26
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.