9RMU | pdb_00009rmu

SIVtal integrase in complex with RNA stem-loop (focused refinement of the filament repeat unit)

PDB DOI: https://doi.org/10.2210/pdb9RMU/pdb
EM Map EMD-54068: EMDB EMDataResource
NAKB: 9RMU

Classification: VIRAL PROTEIN
Organism(s): Simian immunodeficiency virus, Human immunodeficiency virus 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-06-18 Released: 2025-12-10
Deposition Author(s): Singer, M.R., Cherepanov, P.
Funding Organization(s): Cancer Research UK, Medical Research Council (MRC, United Kingdom), Wellcome Trust, The Francis Crick Institute, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 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

Structural basis for integrase-RNA binding and retention of viral RNA within HIV-1 capsid cores

Singer, M.R., Li, Z., Rey, J.S., Hope, J., Cook, N.J., Punch, E., Smith, J., Zhou, Z., Maslen, S., Masino, L., Nans, A., Skehel, M., Taylor, I.A., Zhang, P., Perilla, J.R., Engelman, A.N., Cherepanov, P.

To be published.

Macromolecule Content

Total Structure Weight: 406.83 kDa
Atom Count: 18,876
Modeled Residue Count: 2,254
Deposited Residue Count: 3,188
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pol protein	A B C D F [auth b] A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	296	Simian immunodeficiency virus	Mutation(s): 0 Gene Names: POL
UniProt
Find proteins for Q1XE75 (Simian immunodeficiency virus) Explore Q1XE75 Go to UniProtKB: Q1XE75
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1XE75
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA	E [auth J], K [auth I], M [auth j], N [auth i]	57	Human immunodeficiency virus 1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain X [auth f] SDF format, chain W [auth H] SDF format, chain V [auth G] SDF format, chain U [auth F] SDF format, chain T [auth E] SDF format, chain S [auth b] SDF format, chain R [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth B] SDF format, chain O [auth A] MOL2 format, chain X [auth f] MOL2 format, chain W [auth H] MOL2 format, chain V [auth G] MOL2 format, chain U [auth F] MOL2 format, chain T [auth E] MOL2 format, chain S [auth b] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth A] mmCIF format, chain X [auth f] mmCIF format, chain W [auth H] mmCIF format, chain V [auth G] mmCIF format, chain U [auth F] mmCIF format, chain T [auth E] mmCIF format, chain S [auth b] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth A]	O [auth A] P [auth B] Q [auth C] R [auth D] S [auth b] O [auth A], P [auth B], Q [auth C], R [auth D], S [auth b], T [auth E], U [auth F], V [auth G], W [auth H], X [auth f]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth b] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth f] Interactions & Density Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth b] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth f]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.5.3
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-10

Deposition Author(s):

Singer, M.R.

Cherepanov, P.

Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	CC2058
Medical Research Council (MRC, United Kingdom)	United Kingdom	CC2058
Wellcome Trust	United Kingdom	CC2058
The Francis Crick Institute	United Kingdom	CC2058
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U54AI170791