8K27 | pdb_00008k27

ICP1 Csy-dsDNA complex (partial duplex)

PDB DOI: https://doi.org/10.2210/pdb8K27/pdb
EM Map EMD-36830: EMDB EMDataResource
NAKB: 8K27

Classification: RNA BINDING PROTEIN/DNA/RNA
Organism(s): Vibrio phage ICP1_2004_A
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-07-12 Released: 2024-07-17
Deposition Author(s): Zhang, L.X., Feng, Y.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

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

Literature

Structure of csy complex with short DNA

Zhang, L.X., Feng, Y.

To be published.

Macromolecule Content

Total Structure Weight: 308.9 kDa
Atom Count: 21,183
Modeled Residue Count: 2,530
Deposited Residue Count: 2,565
Unique protein chains: 4
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy1	A	179	Vibrio phage ICP1_2004_A	Mutation(s): 0 Gene Names: TUST1-10_00450
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy2	B	248	Vibrio phage ICP1_2004_A	Mutation(s): 0 Gene Names: TUST1-10_00445
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy3	C [auth D] G [auth C] H [auth G] I [auth F] J [auth E] C [auth D], G [auth C], H [auth G], I [auth F], J [auth E], K [auth H]	306	Vibrio phage ICP1_2004_A	Mutation(s): 0 Gene Names: TUST1-10_00440
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy4	L [auth I]	168	Vibrio phage ICP1_2004_A	Mutation(s): 0 Gene Names: TUST1-10_00435
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (60-MER)	D [auth P]	60	Vibrio phage ICP1_2004_A
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (49-MER)	E [auth Q]	49	Vibrio phage ICP1_2004_A
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	F [auth R]	25	Vibrio phage ICP1_2004_A
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	32171274

Revision History (Full details and data files)

Version 1.0: 2024-07-17
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Structure summary

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.