6X63

Atomic-Resolution Structure of HIV-1 Capsid Tubes by Magic Angle Spinning NMR


Experimental Data Snapshot

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 87 
  • Conformers Submitted: 
  • Selection Criteria: inner turns of helical assembly 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Atomic-resolution structure of HIV-1 capsid tubes by magic-angle spinning NMR.

Lu, M.Russell, R.W.Bryer, A.J.Quinn, C.M.Hou, G.Zhang, H.Schwieters, C.D.Perilla, J.R.Gronenborn, A.M.Polenova, T.

(2020) Nat Struct Mol Biol 27: 863-869

  • DOI: https://doi.org/10.1038/s41594-020-0489-2
  • Primary Citation of Related Structures:  
    6WAP, 6X63

  • PubMed Abstract: 

    HIV-1 capsid plays multiple key roles in viral replication, and inhibition of capsid assembly is an attractive target for therapeutic intervention. Here, we report the atomic-resolution structure of capsid protein (CA) tubes, determined by magic-angle spinning NMR and data-guided molecular dynamics simulations. Functionally important regions, including the NTD β-hairpin, the cyclophilin A-binding loop, residues in the hexamer central pore, and the NTD-CTD linker region, are well defined. The structure of individual CA chains, their arrangement in the pseudo-hexameric units of the tube and the inter-hexamer interfaces are consistent with those in intact capsids and substantially different from the organization in crystal structures, which feature flat hexamers. The inherent curvature in the CA tubes is controlled by conformational variability of residues in the linker region and of dimer and trimer interfaces. The present structure reveals atomic-level detail in capsid architecture and provides important guidance for the design of novel capsid inhibitors.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 capsid protein
A,
AA [auth a],
AB [auth 0],
AC [auth QA],
AD [auth qA],
AE [auth GB],
AF [auth gB],
AG [auth 6B],
AH [auth WC],
AI [auth wC],
AJ [auth MD],
AK [auth mD],
AL [auth CE],
AM [auth cE],
AN [auth 2E],
B,
BA [auth b],
BB [auth 1],
BC [auth RA],
BD [auth rA],
BE [auth HB],
BF [auth hB],
BG [auth 7B],
BH [auth XC],
BI [auth xC],
BJ [auth ND],
BK [auth nD],
BL [auth DE],
BM [auth dE],
BN [auth 3E],
C,
CA [auth c],
CB [auth 2],
CC [auth SA],
CD [auth sA],
CE [auth IB],
CF [auth iB],
CG [auth 8B],
CH [auth YC],
CI [auth yC],
CJ [auth OD],
CK [auth oD],
CL [auth EE],
CM [auth eE],
CN [auth 4E],
D,
DA [auth d],
DB [auth 3],
DC [auth TA],
DD [auth tA],
DE [auth JB],
DF [auth jB],
DG [auth 9B],
DH [auth ZC],
DI [auth zC],
DJ [auth PD],
DK [auth pD],
DL [auth FE],
DM [auth fE],
DN [auth 5E],
E,
EA [auth e],
EB [auth 4],
EC [auth UA],
ED [auth uA],
EE [auth KB],
EF [auth kB],
EG [auth AC],
EH [auth aC],
EI [auth 0C],
EJ [auth QD],
EK [auth qD],
EL [auth GE],
EM [auth gE],
EN [auth 6E],
F,
FA [auth f],
FB [auth 5],
FC [auth VA],
FD [auth vA],
FE [auth LB],
FF [auth lB],
FG [auth BC],
FH [auth bC],
FI [auth 1C],
FJ [auth RD],
FK [auth rD],
FL [auth HE],
FM [auth hE],
FN [auth 7E],
G,
GA [auth g],
GB [auth 6],
GC [auth WA],
GD [auth wA],
GE [auth MB],
GF [auth mB],
GG [auth CC],
GH [auth cC],
GI [auth 2C],
GJ [auth SD],
GK [auth sD],
GL [auth IE],
GM [auth iE],
GN [auth 8E],
H,
HA [auth h],
HB [auth 7],
HC [auth XA],
HD [auth xA],
HE [auth NB],
HF [auth nB],
HG [auth DC],
HH [auth dC],
HI [auth 3C],
HJ [auth TD],
HK [auth tD],
HL [auth JE],
HM [auth jE],
HN [auth 9E],
I,
IA [auth i],
IB [auth 8],
IC [auth YA],
ID [auth yA],
IE [auth OB],
IF [auth oB],
IG [auth EC],
IH [auth eC],
II [auth 4C],
IJ [auth UD],
IK [auth uD],
IL [auth KE],
IM [auth kE],
IN [auth AF],
J,
JA [auth j],
JB [auth 9],
JC [auth ZA],
JD [auth zA],
JE [auth PB],
JF [auth pB],
JG [auth FC],
JH [auth fC],
JI [auth 5C],
JJ [auth VD],
JK [auth vD],
JL [auth LE],
JM [auth lE],
JN [auth BF],
K,
KA [auth k],
KB [auth AA],
KC [auth aA],
KD [auth 0A],
KE [auth QB],
KF [auth qB],
KG [auth GC],
KH [auth gC],
KI [auth 6C],
KJ [auth WD],
KK [auth wD],
KL [auth ME],
KM [auth mE],
KN [auth CF],
L,
LA [auth l],
LB [auth BA],
LC [auth bA],
LD [auth 1A],
LE [auth RB],
LF [auth rB],
LG [auth HC],
LH [auth hC],
LI [auth 7C],
LJ [auth XD],
LK [auth xD],
LL [auth NE],
LM [auth nE],
LN [auth DF],
M,
MA [auth m],
MB [auth CA],
MC [auth cA],
MD [auth 2A],
ME [auth SB],
MF [auth sB],
MG [auth IC],
MH [auth iC],
MI [auth 8C],
MJ [auth YD],
MK [auth yD],
ML [auth OE],
MM [auth oE],
MN [auth EF],
N,
NA [auth n],
NB [auth DA],
NC [auth dA],
ND [auth 3A],
NE [auth TB],
NF [auth tB],
NG [auth JC],
NH [auth jC],
NI [auth 9C],
NJ [auth ZD],
NK [auth zD],
NL [auth PE],
NM [auth pE],
NN [auth FF],
O,
OA [auth o],
OB [auth EA],
OC [auth eA],
OD [auth 4A],
OE [auth UB],
OF [auth uB],
OG [auth KC],
OH [auth kC],
OI [auth AD],
OJ [auth aD],
OK [auth 0D],
OL [auth QE],
OM [auth qE],
P,
PA [auth p],
PB [auth FA],
PC [auth fA],
PD [auth 5A],
PE [auth VB],
PF [auth vB],
PG [auth LC],
PH [auth lC],
PI [auth BD],
PJ [auth bD],
PK [auth 1D],
PL [auth RE],
PM [auth rE],
Q,
QA [auth q],
QB [auth GA],
QC [auth gA],
QD [auth 6A],
QE [auth WB],
QF [auth wB],
QG [auth MC],
QH [auth mC],
QI [auth CD],
QJ [auth cD],
QK [auth 2D],
QL [auth SE],
QM [auth sE],
R,
RA [auth r],
RB [auth HA],
RC [auth hA],
RD [auth 7A],
RE [auth XB],
RF [auth xB],
RG [auth NC],
RH [auth nC],
RI [auth DD],
RJ [auth dD],
RK [auth 3D],
RL [auth TE],
RM [auth tE],
S,
SA [auth s],
SB [auth IA],
SC [auth iA],
SD [auth 8A],
SE [auth YB],
SF [auth yB],
SG [auth OC],
SH [auth oC],
SI [auth ED],
SJ [auth eD],
SK [auth 4D],
SL [auth UE],
SM [auth uE],
T,
TA [auth t],
TB [auth JA],
TC [auth jA],
TD [auth 9A],
TE [auth ZB],
TF [auth zB],
TG [auth PC],
TH [auth pC],
TI [auth FD],
TJ [auth fD],
TK [auth 5D],
TL [auth VE],
TM [auth vE],
U,
UA [auth u],
UB [auth KA],
UC [auth kA],
UD [auth AB],
UE [auth aB],
UF [auth 0B],
UG [auth QC],
UH [auth qC],
UI [auth GD],
UJ [auth gD],
UK [auth 6D],
UL [auth WE],
UM [auth wE],
V,
VA [auth v],
VB [auth LA],
VC [auth lA],
VD [auth BB],
VE [auth bB],
VF [auth 1B],
VG [auth RC],
VH [auth rC],
VI [auth HD],
VJ [auth hD],
VK [auth 7D],
VL [auth XE],
VM [auth xE],
W,
WA [auth w],
WB [auth MA],
WC [auth mA],
WD [auth CB],
WE [auth cB],
WF [auth 2B],
WG [auth SC],
WH [auth sC],
WI [auth ID],
WJ [auth iD],
WK [auth 8D],
WL [auth YE],
WM [auth yE],
X,
XA [auth x],
XB [auth NA],
XC [auth nA],
XD [auth DB],
XE [auth dB],
XF [auth 3B],
XG [auth TC],
XH [auth tC],
XI [auth JD],
XJ [auth jD],
XK [auth 9D],
XL [auth ZE],
XM [auth zE],
Y,
YA [auth y],
YB [auth OA],
YC [auth oA],
YD [auth EB],
YE [auth eB],
YF [auth 4B],
YG [auth UC],
YH [auth uC],
YI [auth KD],
YJ [auth kD],
YK [auth AE],
YL [auth aE],
YM [auth 0E],
Z,
ZA [auth z],
ZB [auth PA],
ZC [auth pA],
ZD [auth FB],
ZE [auth fB],
ZF [auth 5B],
ZG [auth VC],
ZH [auth vC],
ZI [auth LD],
ZJ [auth lD],
ZK [auth BE],
ZL [auth bE],
ZM [auth 1E]
231Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: Gag-pol
UniProt
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12493 
Go to UniProtKB:  P12493
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12493
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 87 
  • Conformers Submitted: 
  • Selection Criteria: inner turns of helical assembly 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP50AI1504817
National Science Foundation (NSF, United States)United StatesCHE0959496
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM110758
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD012213

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2021-11-03
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2023-06-14
    Changes: Other