9RAE | pdb_00009rae

PhiC31 integrase-attL complex: P'-bound subregion

PDB DOI: https://doi.org/10.2210/pdb9RAE/pdb
NAKB: 9RAE
EM Map EMD-53875: EMDB EMDataResource

Classification: DNA BINDING PROTEIN
Organism(s): Lomovskayavirus C31
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-05-20 Released: 2026-02-11
Deposition Author(s): Sun, Y.E., Spagnolo, L.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.88 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9RAE

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

Literature

Structural mechanisms of unidirectional prophage integration and excision by serine integrases

Sun, Y.E., Aspinall, L., Joseph, A.P., Colloms, S.D., Stark, W.M., Spagnolo, L.

To be published.

Macromolecule Content

Total Structure Weight: 175.85 kDa
Atom Count: 5,038
Modeled Residue Count: 557
Deposited Residue Count: 1,370
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A [auth B], D [auth A]	625	Lomovskayavirus C31	Mutation(s): 0 Gene Names: int
UniProt
Find proteins for Q9T221 (Streptomyces phage phiC31) Explore Q9T221 Go to UniProtKB: Q9T221
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9T221
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 2
attL_Fw	B [auth E]	60	Lomovskayavirus C31
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 3
attL_Rv	C [auth F]	60	Lomovskayavirus C31
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.88 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/W017571/1

Revision History (Full details and data files)

Version 1.0: 2026-02-11
Type: Initial release

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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.