9RMX | pdb_00009rmx

CryoEM reconstruction of integrase filament at the lumen of native HIV-1 cores (box size 34.2 nm)

PDB DOI: https://doi.org/10.2210/pdb9RMX/pdb
EM Map EMD-54071: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Human immunodeficiency virus 1
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-06-19 Released: 2025-12-10
Deposition Author(s): Cherepanov, P., Singer, M.R., Hope, J., Zhang, P.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Wellcome Trust, Medical Research Council (MRC, United Kingdom), Cancer Research UK

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.63 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

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

Singer, M., 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: 1,213.15 kDa
Atom Count: 72,751
Modeled Residue Count: 9,257
Deposited Residue Count: 10,848
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	288	Human immunodeficiency virus 1	Mutation(s): 2 Gene Names: gag-pol EC: 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497 Go to UniProtKB: P12497
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12497
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag polyprotein	AA [auth i] BA [auth j] CA [auth k] DA [auth l] EA [auth m] AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], FA [auth n], GA [auth o], HA [auth p], IA [auth q], JA [auth r], KA [auth s], LA [auth t], M [auth U], MA [auth u], N [auth V], NA [auth v], O [auth W], OA [auth w], P [auth X], PA [auth x], Q [auth Y], QA [auth y], R [auth Z], RA [auth z], S [auth a], T [auth b], U [auth c], V [auth d], W [auth e], X [auth f], Y [auth g], Z [auth h]	231	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: gag
UniProt
Find proteins for Q72497 (Human immunodeficiency virus type 1) Explore Q72497 Go to UniProtKB: Q72497
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q72497
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IHP Query on IHP Download Ideal Coordinates CCD File SDF format, chain LB [auth q] SDF format, chain KB [auth m] SDF format, chain JB [auth i] SDF format, chain IB [auth g] SDF format, chain HB [auth b] SDF format, chain GB [auth a] SDF format, chain FB [auth Z] SDF format, chain EB [auth X] MOL2 format, chain LB [auth q] MOL2 format, chain KB [auth m] MOL2 format, chain JB [auth i] MOL2 format, chain IB [auth g] MOL2 format, chain HB [auth b] MOL2 format, chain GB [auth a] MOL2 format, chain FB [auth Z] MOL2 format, chain EB [auth X] mmCIF format, chain LB [auth q] mmCIF format, chain KB [auth m] mmCIF format, chain JB [auth i] mmCIF format, chain IB [auth g] mmCIF format, chain HB [auth b] mmCIF format, chain GB [auth a] mmCIF format, chain FB [auth Z] mmCIF format, chain EB [auth X]	EB [auth X] FB [auth Z] GB [auth a] HB [auth b] IB [auth g] EB [auth X], FB [auth Z], GB [auth a], HB [auth b], IB [auth g], JB [auth i], KB [auth m], LB [auth q]	INOSITOL HEXAKISPHOSPHATE C₆ H₁₈ O₂₄ P₆ IMQLKJBTEOYOSI-GPIVLXJGSA-N		Interactions Focus chain EB [auth X] Focus chain FB [auth Z] Focus chain GB [auth a] Focus chain HB [auth b] Focus chain IB [auth g] Focus chain JB [auth i] Focus chain KB [auth m] Focus chain LB [auth q] Interactions & Density Focus chain EB [auth X] Focus chain FB [auth Z] Focus chain GB [auth a] Focus chain HB [auth b] Focus chain IB [auth g] Focus chain JB [auth i] Focus chain KB [auth m] Focus chain LB [auth q]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain ZA [auth H] SDF format, chain YA [auth G] SDF format, chain XA [auth F] SDF format, chain WA [auth E] SDF format, chain VA [auth D] SDF format, chain UA [auth C] SDF format, chain TA [auth B] SDF format, chain SA [auth A] SDF format, chain DB [auth L] SDF format, chain CB [auth K] SDF format, chain BB [auth J] SDF format, chain AB [auth I] MOL2 format, chain ZA [auth H] MOL2 format, chain YA [auth G] MOL2 format, chain XA [auth F] MOL2 format, chain WA [auth E] MOL2 format, chain VA [auth D] MOL2 format, chain UA [auth C] MOL2 format, chain TA [auth B] MOL2 format, chain SA [auth A] MOL2 format, chain DB [auth L] MOL2 format, chain CB [auth K] MOL2 format, chain BB [auth J] MOL2 format, chain AB [auth I] mmCIF format, chain ZA [auth H] mmCIF format, chain YA [auth G] mmCIF format, chain XA [auth F] mmCIF format, chain WA [auth E] mmCIF format, chain VA [auth D] mmCIF format, chain UA [auth C] mmCIF format, chain TA [auth B] mmCIF format, chain SA [auth A] mmCIF format, chain DB [auth L] mmCIF format, chain CB [auth K] mmCIF format, chain BB [auth J] mmCIF format, chain AB [auth I]	AB [auth I] BB [auth J] CB [auth K] DB [auth L] SA [auth A] AB [auth I], BB [auth J], CB [auth K], DB [auth L], SA [auth A], TA [auth B], UA [auth C], VA [auth D], WA [auth E], XA [auth F], YA [auth G], ZA [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth I] Focus chain BB [auth J] Focus chain CB [auth K] Focus chain DB [auth L] Focus chain SA [auth A] Focus chain TA [auth B] Focus chain UA [auth C] Focus chain VA [auth D] Focus chain WA [auth E] Focus chain XA [auth F] Focus chain YA [auth G] Focus chain ZA [auth H] Interactions & Density Focus chain AB [auth I] Focus chain BB [auth J] Focus chain CB [auth K] Focus chain DB [auth L] Focus chain SA [auth A] Focus chain TA [auth B] Focus chain UA [auth C] Focus chain VA [auth D] Focus chain WA [auth E] Focus chain XA [auth F] Focus chain YA [auth G] Focus chain ZA [auth H]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.63 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6.2
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):

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