8GIU | pdb_00008giu

Mycobacterium phage Patience

PDB DOI: https://doi.org/10.2210/pdb8GIU/pdb
EM Map EMD-40077: EMDB EMDataResource

Classification: VIRUS
Organism(s): Mycobacterium phage Patience
Mutation(s): No

Deposited: 2023-03-14 Released: 2023-05-24
Deposition Author(s): Podgorski, J.M., White, S.J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.39 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8GIU

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

Literature

A novel accessory protein stabilizes the capsid of two actinobacteriophages

Podgorski, J.M., Porgorski, J., Gosselin, S., Abad, L., Jacobs-Sera, D., Brown, C., Hatfull, G., Gogarten, P., Luque, A., White, S.J.

To be published.

Macromolecule Content

Total Structure Weight: 494.93 kDa
Atom Count: 33,694
Modeled Residue Count: 4,467
Deposited Residue Count: 4,628
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gp_4 (capsid accessory protein)	A [auth Z], B [auth Y]	102	Mycobacterium phage Patience	Mutation(s): 0
UniProt
Find proteins for G1JWB5 (Mycobacterium phage Patience) Explore G1JWB5 Go to UniProtKB: G1JWB5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1JWB5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	C [auth E] D [auth F] E [auth A] F [auth B] G [auth C] C [auth E], D [auth F], E [auth A], F [auth B], G [auth C], H [auth D], I [auth G]	400	Mycobacterium phage Patience	Mutation(s): 0
UniProt
Find proteins for G1JWD4 (Mycobacterium phage Patience) Explore G1JWD4 Go to UniProtKB: G1JWD4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1JWD4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
gp_22 (Minor Capsid Protein)	J [auth 1] K [auth 2] L [auth 3] M [auth 4] N [auth 5] J [auth 1], K [auth 2], L [auth 3], M [auth 4], N [auth 5], O [auth 6], P [auth 7]	232	Mycobacterium phage Patience	Mutation(s): 0
UniProt
Find proteins for G1JWD3 (Mycobacterium phage Patience) Explore G1JWD3 Go to UniProtKB: G1JWD3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1JWD3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.39 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1
MODEL REFINEMENT	ISOLDE	1.3
RECONSTRUCTION	RELION	3.1.0

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-05-24

Deposition Author(s):

Podgorski, J.M.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-05-24
Type: Initial release
Version 1.1: 2024-06-19
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.