9EK2

HIV-1 immature L20K/E73K/A82T matrix protein p17 lattice

PDB DOI: https://doi.org/10.2210/pdb9EK2/pdb
EM Map EMD-52059: EMDB EMDataResource

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

Deposited: 2024-11-30 Released: 2025-01-08
Deposition Author(s): Rey, J.S., Perilla, J.R., Chen, L., Zhang, P.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 8.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SUBTOMOGRAM AVERAGING

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 maturation of the matrix lattice is not required for HIV-1 particle infectivity

Rey, J.S., Perilla, J.R., Chen, L., Zhang, P.

To be published.

Macromolecule Content

Total Structure Weight: 521.02 kDa
Atom Count: 36,504
Modelled Residue Count: 4,485
Deposited Residue Count: 4,485
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix protein p17	A AA [auth C] B [auth D] BA [auth F] C [auth e] A, AA [auth C], B [auth D], BA [auth F], C [auth e], CA [auth g], D [auth h], DA [auth j], E [auth k], EA [auth m], F [auth G], FA [auth I], G [auth J], GA [auth L], H [auth M], HA [auth O], I [auth P], IA [auth R], J [auth S], JA [auth U], K [auth V], KA [auth X], L [auth Y], LA [auth a], M [auth b], MA [auth d], N [auth B], O [auth E], P [auth f], Q [auth i], R [auth l], S [auth H], T [auth K], U [auth N], V [auth Q], W [auth T], X [auth W], Y [auth Z], Z [auth c]	115	Human immunodeficiency virus 1	Mutation(s): 3 Gene Names: gag-pol
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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MYR Query on MYR Download Ideal Coordinates CCD File SDF format, chain OA [auth D] SDF format, chain VB [auth R] SDF format, chain WB [auth U] SDF format, chain AB [auth B] SDF format, chain BB [auth E] SDF format, chain CB [auth f] SDF format, chain DB [auth i] SDF format, chain EB [auth l] SDF format, chain FB [auth H] SDF format, chain GB [auth K] SDF format, chain HB [auth N] SDF format, chain IB [auth Q] SDF format, chain JB [auth T] SDF format, chain KB [auth W] SDF format, chain LB [auth Z] SDF format, chain MB [auth c] SDF format, chain NA [auth A] SDF format, chain NB [auth C] SDF format, chain OB [auth F] SDF format, chain PA [auth e] SDF format, chain PB [auth g] SDF format, chain QA [auth h] SDF format, chain QB [auth j] SDF format, chain RA [auth k] SDF format, chain RB [auth m] SDF format, chain SA [auth G] SDF format, chain SB [auth I] SDF format, chain TA [auth J] SDF format, chain TB [auth L] SDF format, chain UA [auth M] SDF format, chain UB [auth O] SDF format, chain VA [auth P] SDF format, chain WA [auth S] SDF format, chain XA [auth V] SDF format, chain XB [auth X] SDF format, chain YA [auth Y] SDF format, chain YB [auth a] SDF format, chain ZA [auth b] SDF format, chain ZB [auth d] MOL2 format, chain OA [auth D] MOL2 format, chain VB [auth R] MOL2 format, chain WB [auth U] MOL2 format, chain AB [auth B] MOL2 format, chain BB [auth E] MOL2 format, chain CB [auth f] MOL2 format, chain DB [auth i] MOL2 format, chain EB [auth l] MOL2 format, chain FB [auth H] MOL2 format, chain GB [auth K] MOL2 format, chain HB [auth N] MOL2 format, chain IB [auth Q] MOL2 format, chain JB [auth T] MOL2 format, chain KB [auth W] MOL2 format, chain LB [auth Z] MOL2 format, chain MB [auth c] MOL2 format, chain NA [auth A] MOL2 format, chain NB [auth C] MOL2 format, chain OB [auth F] MOL2 format, chain PA [auth e] MOL2 format, chain PB [auth g] MOL2 format, chain QA [auth h] MOL2 format, chain QB [auth j] MOL2 format, chain RA [auth k] MOL2 format, chain RB [auth m] MOL2 format, chain SA [auth G] MOL2 format, chain SB [auth I] MOL2 format, chain TA [auth J] MOL2 format, chain TB [auth L] MOL2 format, chain UA [auth M] MOL2 format, chain UB [auth O] MOL2 format, chain VA [auth P] MOL2 format, chain WA [auth S] MOL2 format, chain XA [auth V] MOL2 format, chain XB [auth X] MOL2 format, chain YA [auth Y] MOL2 format, chain YB [auth a] MOL2 format, chain ZA [auth b] MOL2 format, chain ZB [auth d] mmCIF format, chain OA [auth D] mmCIF format, chain VB [auth R] mmCIF format, chain WB [auth U] mmCIF format, chain AB [auth B] mmCIF format, chain BB [auth E] mmCIF format, chain CB [auth f] mmCIF format, chain DB [auth i] mmCIF format, chain EB [auth l] mmCIF format, chain FB [auth H] mmCIF format, chain GB [auth K] mmCIF format, chain HB [auth N] mmCIF format, chain IB [auth Q] mmCIF format, chain JB [auth T] mmCIF format, chain KB [auth W] mmCIF format, chain LB [auth Z] mmCIF format, chain MB [auth c] mmCIF format, chain NA [auth A] mmCIF format, chain NB [auth C] mmCIF format, chain OB [auth F] mmCIF format, chain PA [auth e] mmCIF format, chain PB [auth g] mmCIF format, chain QA [auth h] mmCIF format, chain QB [auth j] mmCIF format, chain RA [auth k] mmCIF format, chain RB [auth m] mmCIF format, chain SA [auth G] mmCIF format, chain SB [auth I] mmCIF format, chain TA [auth J] mmCIF format, chain TB [auth L] mmCIF format, chain UA [auth M] mmCIF format, chain UB [auth O] mmCIF format, chain VA [auth P] mmCIF format, chain WA [auth S] mmCIF format, chain XA [auth V] mmCIF format, chain XB [auth X] mmCIF format, chain YA [auth Y] mmCIF format, chain YB [auth a] mmCIF format, chain ZA [auth b] mmCIF format, chain ZB [auth d]	AB [auth B] BB [auth E] CB [auth f] DB [auth i] EB [auth l] AB [auth B], BB [auth E], CB [auth f], DB [auth i], EB [auth l], FB [auth H], GB [auth K], HB [auth N], IB [auth Q], JB [auth T], KB [auth W], LB [auth Z], MB [auth c], NA [auth A], NB [auth C], OA [auth D], OB [auth F], PA [auth e], PB [auth g], QA [auth h], QB [auth j], RA [auth k], RB [auth m], SA [auth G], SB [auth I], TA [auth J], TB [auth L], UA [auth M], UB [auth O], VA [auth P], VB [auth R], WA [auth S], WB [auth U], XA [auth V], XB [auth X], YA [auth Y], YB [auth a], ZA [auth b], ZB [auth d]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain BB [auth E] Focus chain CB [auth f] Focus chain DB [auth i] Focus chain EB [auth l] Focus chain FB [auth H] Focus chain GB [auth K] Focus chain HB [auth N] Focus chain IB [auth Q] Focus chain JB [auth T] Focus chain KB [auth W] Focus chain LB [auth Z] Focus chain MB [auth c] Focus chain NA [auth A] Focus chain NB [auth C] Focus chain OA [auth D] Focus chain OB [auth F] Focus chain PA [auth e] Focus chain PB [auth g] Focus chain QA [auth h] Focus chain QB [auth j] Focus chain RA [auth k] Focus chain RB [auth m] Focus chain SA [auth G] Focus chain SB [auth I] Focus chain TA [auth J] Focus chain TB [auth L] Focus chain UA [auth M] Focus chain UB [auth O] Focus chain VA [auth P] Focus chain VB [auth R] Focus chain WA [auth S] Focus chain WB [auth U] Focus chain XA [auth V] Focus chain XB [auth X] Focus chain YA [auth Y] Focus chain YB [auth a] Focus chain ZA [auth b] Focus chain ZB [auth d] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth E] Focus chain CB [auth f] Focus chain DB [auth i] Focus chain EB [auth l] Focus chain FB [auth H] Focus chain GB [auth K] Focus chain HB [auth N] Focus chain IB [auth Q] Focus chain JB [auth T] Focus chain KB [auth W] Focus chain LB [auth Z] Focus chain MB [auth c] Focus chain NA [auth A] Focus chain NB [auth C] Focus chain OA [auth D] Focus chain OB [auth F] Focus chain PA [auth e] Focus chain PB [auth g] Focus chain QA [auth h] Focus chain QB [auth j] Focus chain RA [auth k] Focus chain RB [auth m] Focus chain SA [auth G] Focus chain SB [auth I] Focus chain TA [auth J] Focus chain TB [auth L] Focus chain UA [auth M] Focus chain UB [auth O] Focus chain VA [auth P] Focus chain VB [auth R] Focus chain WA [auth S] Focus chain WB [auth U] Focus chain XA [auth V] Focus chain XB [auth X] Focus chain YA [auth Y] Focus chain YB [auth a] Focus chain ZA [auth b] Focus chain ZB [auth d]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 8.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SUBTOMOGRAM AVERAGING

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	NAMD	3.0
MODEL REFINEMENT	Rosetta	3.14

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI178846
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21AI184080
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI150560