8F2M

Phi-29 scaffolding protein bound to intermediate-state MCP

PDB DOI: https://doi.org/10.2210/pdb8F2M/pdb
EM Map EMD-28822: EMDB EMDataResource

Classification: VIRUS
Organism(s): Bacillus phage phi29
Expression System: Escherichia phage EcSzw-2
Mutation(s): No

Deposited: 2022-11-08 Released: 2023-11-15
Deposition Author(s): Woodson, M.E., Morais, M.C., Jardine, P.J., Scott, S.D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Scaffold Oligomers Control Prohead Expansion

Woodson, M.E., Morais, M.C., Prokhorov, N.S., Scott, S.D., Zhang, W., Choi, K.H., Jardine, P.J.

To be published.

Macromolecule Content

Total Structure Weight: 83.74 kDa
Atom Count: 4,696
Modelled Residue Count: 592
Deposited Residue Count: 742
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A [auth D]	448	Bacillus phage phi29	Mutation(s): 0
UniProt
Find proteins for P13849 (Bacillus phage phi29) Explore P13849 Go to UniProtKB: P13849
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13849
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid assembly scaffolding protein	B [auth F], C [auth B], D [auth C]	98	Bacillus phage phi29	Mutation(s): 0
UniProt
Find proteins for P13848 (Bacillus phage phi29) Explore P13848 Go to UniProtKB: P13848
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13848
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19
RECONSTRUCTION	RELION	3.0

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM122979

Revision History (Full details and data files)

Version 1.0: 2023-11-15
Type: Initial release

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.