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- PDB-6x63: Atomic-Resolution Structure of HIV-1 Capsid Tubes by Magic Angle ... -

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Basic information

Entry
Database: PDB / ID: 6x63
TitleAtomic-Resolution Structure of HIV-1 Capsid Tubes by Magic Angle Spinning NMR
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / magic angle spinning NMR / HIV-1 capsid / CA protein assemblies / HIV-AIDS
Function / homology
Function and homology information


viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein ...Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodSOLID-STATE NMR / data-guided molecular dynamics
AuthorsLu, M. / Russell, R.W. / Bryer, A. / Quinn, C.M. / Hou, G. / Zhang, H. / Schwieters, C.D. / Perilla, J.R. / Gronenborn, A.M. / Polenova, T.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50AI1504817 United States
National Science Foundation (NSF, United States)CHE0959496 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110758 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD012213 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: Atomic-resolution structure of HIV-1 capsid tubes by magic-angle spinning NMR.
Authors: 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.
History
DepositionMay 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 3, 2021Group: Data collection / Database references / Refinement description
Category: database_2 / pdbx_nmr_refine / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_refine.software_ordinal
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 capsid protein
B: HIV-1 capsid protein
C: HIV-1 capsid protein
D: HIV-1 capsid protein
E: HIV-1 capsid protein
F: HIV-1 capsid protein
G: HIV-1 capsid protein
H: HIV-1 capsid protein
I: HIV-1 capsid protein
J: HIV-1 capsid protein
K: HIV-1 capsid protein
L: HIV-1 capsid protein
M: HIV-1 capsid protein
N: HIV-1 capsid protein
O: HIV-1 capsid protein
P: HIV-1 capsid protein
Q: HIV-1 capsid protein
R: HIV-1 capsid protein
S: HIV-1 capsid protein
T: HIV-1 capsid protein
U: HIV-1 capsid protein
V: HIV-1 capsid protein
W: HIV-1 capsid protein
X: HIV-1 capsid protein
Y: HIV-1 capsid protein
Z: HIV-1 capsid protein
a: HIV-1 capsid protein
b: HIV-1 capsid protein
c: HIV-1 capsid protein
d: HIV-1 capsid protein
e: HIV-1 capsid protein
f: HIV-1 capsid protein
g: HIV-1 capsid protein
h: HIV-1 capsid protein
i: HIV-1 capsid protein
j: HIV-1 capsid protein
k: HIV-1 capsid protein
l: HIV-1 capsid protein
m: HIV-1 capsid protein
n: HIV-1 capsid protein
o: HIV-1 capsid protein
p: HIV-1 capsid protein
q: HIV-1 capsid protein
r: HIV-1 capsid protein
s: HIV-1 capsid protein
t: HIV-1 capsid protein
u: HIV-1 capsid protein
v: HIV-1 capsid protein
w: HIV-1 capsid protein
x: HIV-1 capsid protein
y: HIV-1 capsid protein
z: HIV-1 capsid protein
0: HIV-1 capsid protein
1: HIV-1 capsid protein
2: HIV-1 capsid protein
3: HIV-1 capsid protein
4: HIV-1 capsid protein
5: HIV-1 capsid protein
6: HIV-1 capsid protein
7: HIV-1 capsid protein
8: HIV-1 capsid protein
9: HIV-1 capsid protein
AA: HIV-1 capsid protein
BA: HIV-1 capsid protein
CA: HIV-1 capsid protein
DA: HIV-1 capsid protein
EA: HIV-1 capsid protein
FA: HIV-1 capsid protein
GA: HIV-1 capsid protein
HA: HIV-1 capsid protein
IA: HIV-1 capsid protein
JA: HIV-1 capsid protein
KA: HIV-1 capsid protein
LA: HIV-1 capsid protein
MA: HIV-1 capsid protein
NA: HIV-1 capsid protein
OA: HIV-1 capsid protein
PA: HIV-1 capsid protein
QA: HIV-1 capsid protein
RA: HIV-1 capsid protein
SA: HIV-1 capsid protein
TA: HIV-1 capsid protein
UA: HIV-1 capsid protein
VA: HIV-1 capsid protein
WA: HIV-1 capsid protein
XA: HIV-1 capsid protein
YA: HIV-1 capsid protein
ZA: HIV-1 capsid protein
aA: HIV-1 capsid protein
bA: HIV-1 capsid protein
cA: HIV-1 capsid protein
dA: HIV-1 capsid protein
eA: HIV-1 capsid protein
fA: HIV-1 capsid protein
gA: HIV-1 capsid protein
hA: HIV-1 capsid protein
iA: HIV-1 capsid protein
jA: HIV-1 capsid protein
kA: HIV-1 capsid protein
lA: HIV-1 capsid protein
mA: HIV-1 capsid protein
nA: HIV-1 capsid protein
oA: HIV-1 capsid protein
pA: HIV-1 capsid protein
qA: HIV-1 capsid protein
rA: HIV-1 capsid protein
sA: HIV-1 capsid protein
tA: HIV-1 capsid protein
uA: HIV-1 capsid protein
vA: HIV-1 capsid protein
wA: HIV-1 capsid protein
xA: HIV-1 capsid protein
yA: HIV-1 capsid protein
zA: HIV-1 capsid protein
0A: HIV-1 capsid protein
1A: HIV-1 capsid protein
2A: HIV-1 capsid protein
3A: HIV-1 capsid protein
4A: HIV-1 capsid protein
5A: HIV-1 capsid protein
6A: HIV-1 capsid protein
7A: HIV-1 capsid protein
8A: HIV-1 capsid protein
9A: HIV-1 capsid protein
AB: HIV-1 capsid protein
BB: HIV-1 capsid protein
CB: HIV-1 capsid protein
DB: HIV-1 capsid protein
EB: HIV-1 capsid protein
FB: HIV-1 capsid protein
GB: HIV-1 capsid protein
HB: HIV-1 capsid protein
IB: HIV-1 capsid protein
JB: HIV-1 capsid protein
KB: HIV-1 capsid protein
LB: HIV-1 capsid protein
MB: HIV-1 capsid protein
NB: HIV-1 capsid protein
OB: HIV-1 capsid protein
PB: HIV-1 capsid protein
QB: HIV-1 capsid protein
RB: HIV-1 capsid protein
SB: HIV-1 capsid protein
TB: HIV-1 capsid protein
UB: HIV-1 capsid protein
VB: HIV-1 capsid protein
WB: HIV-1 capsid protein
XB: HIV-1 capsid protein
YB: HIV-1 capsid protein
ZB: HIV-1 capsid protein
aB: HIV-1 capsid protein
bB: HIV-1 capsid protein
cB: HIV-1 capsid protein
dB: HIV-1 capsid protein
eB: HIV-1 capsid protein
fB: HIV-1 capsid protein
gB: HIV-1 capsid protein
hB: HIV-1 capsid protein
iB: HIV-1 capsid protein
jB: HIV-1 capsid protein
kB: HIV-1 capsid protein
lB: HIV-1 capsid protein
mB: HIV-1 capsid protein
nB: HIV-1 capsid protein
oB: HIV-1 capsid protein
pB: HIV-1 capsid protein
qB: HIV-1 capsid protein
rB: HIV-1 capsid protein
sB: HIV-1 capsid protein
tB: HIV-1 capsid protein
uB: HIV-1 capsid protein
vB: HIV-1 capsid protein
wB: HIV-1 capsid protein
xB: HIV-1 capsid protein
yB: HIV-1 capsid protein
zB: HIV-1 capsid protein
0B: HIV-1 capsid protein
1B: HIV-1 capsid protein
2B: HIV-1 capsid protein
3B: HIV-1 capsid protein
4B: HIV-1 capsid protein
5B: HIV-1 capsid protein
6B: HIV-1 capsid protein
7B: HIV-1 capsid protein
8B: HIV-1 capsid protein
9B: HIV-1 capsid protein
AC: HIV-1 capsid protein
BC: HIV-1 capsid protein
CC: HIV-1 capsid protein
DC: HIV-1 capsid protein
EC: HIV-1 capsid protein
FC: HIV-1 capsid protein
GC: HIV-1 capsid protein
HC: HIV-1 capsid protein
IC: HIV-1 capsid protein
JC: HIV-1 capsid protein
KC: HIV-1 capsid protein
LC: HIV-1 capsid protein
MC: HIV-1 capsid protein
NC: HIV-1 capsid protein
OC: HIV-1 capsid protein
PC: HIV-1 capsid protein
QC: HIV-1 capsid protein
RC: HIV-1 capsid protein
SC: HIV-1 capsid protein
TC: HIV-1 capsid protein
UC: HIV-1 capsid protein
VC: HIV-1 capsid protein
WC: HIV-1 capsid protein
XC: HIV-1 capsid protein
YC: HIV-1 capsid protein
ZC: HIV-1 capsid protein
aC: HIV-1 capsid protein
bC: HIV-1 capsid protein
cC: HIV-1 capsid protein
dC: HIV-1 capsid protein
eC: HIV-1 capsid protein
fC: HIV-1 capsid protein
gC: HIV-1 capsid protein
hC: HIV-1 capsid protein
iC: HIV-1 capsid protein
jC: HIV-1 capsid protein
kC: HIV-1 capsid protein
lC: HIV-1 capsid protein
mC: HIV-1 capsid protein
nC: HIV-1 capsid protein
oC: HIV-1 capsid protein
pC: HIV-1 capsid protein
qC: HIV-1 capsid protein
rC: HIV-1 capsid protein
sC: HIV-1 capsid protein
tC: HIV-1 capsid protein
uC: HIV-1 capsid protein
vC: HIV-1 capsid protein
wC: HIV-1 capsid protein
xC: HIV-1 capsid protein
yC: HIV-1 capsid protein
zC: HIV-1 capsid protein
0C: HIV-1 capsid protein
1C: HIV-1 capsid protein
2C: HIV-1 capsid protein
3C: HIV-1 capsid protein
4C: HIV-1 capsid protein
5C: HIV-1 capsid protein
6C: HIV-1 capsid protein
7C: HIV-1 capsid protein
8C: HIV-1 capsid protein
9C: HIV-1 capsid protein
AD: HIV-1 capsid protein
BD: HIV-1 capsid protein
CD: HIV-1 capsid protein
DD: HIV-1 capsid protein
ED: HIV-1 capsid protein
FD: HIV-1 capsid protein
GD: HIV-1 capsid protein
HD: HIV-1 capsid protein
ID: HIV-1 capsid protein
JD: HIV-1 capsid protein
KD: HIV-1 capsid protein
LD: HIV-1 capsid protein
MD: HIV-1 capsid protein
ND: HIV-1 capsid protein
OD: HIV-1 capsid protein
PD: HIV-1 capsid protein
QD: HIV-1 capsid protein
RD: HIV-1 capsid protein
SD: HIV-1 capsid protein
TD: HIV-1 capsid protein
UD: HIV-1 capsid protein
VD: HIV-1 capsid protein
WD: HIV-1 capsid protein
XD: HIV-1 capsid protein
YD: HIV-1 capsid protein
ZD: HIV-1 capsid protein
aD: HIV-1 capsid protein
bD: HIV-1 capsid protein
cD: HIV-1 capsid protein
dD: HIV-1 capsid protein
eD: HIV-1 capsid protein
fD: HIV-1 capsid protein
gD: HIV-1 capsid protein
hD: HIV-1 capsid protein
iD: HIV-1 capsid protein
jD: HIV-1 capsid protein
kD: HIV-1 capsid protein
lD: HIV-1 capsid protein
mD: HIV-1 capsid protein
nD: HIV-1 capsid protein
oD: HIV-1 capsid protein
pD: HIV-1 capsid protein
qD: HIV-1 capsid protein
rD: HIV-1 capsid protein
sD: HIV-1 capsid protein
tD: HIV-1 capsid protein
uD: HIV-1 capsid protein
vD: HIV-1 capsid protein
wD: HIV-1 capsid protein
xD: HIV-1 capsid protein
yD: HIV-1 capsid protein
zD: HIV-1 capsid protein
0D: HIV-1 capsid protein
1D: HIV-1 capsid protein
2D: HIV-1 capsid protein
3D: HIV-1 capsid protein
4D: HIV-1 capsid protein
5D: HIV-1 capsid protein
6D: HIV-1 capsid protein
7D: HIV-1 capsid protein
8D: HIV-1 capsid protein
9D: HIV-1 capsid protein
AE: HIV-1 capsid protein
BE: HIV-1 capsid protein
CE: HIV-1 capsid protein
DE: HIV-1 capsid protein
EE: HIV-1 capsid protein
FE: HIV-1 capsid protein
GE: HIV-1 capsid protein
HE: HIV-1 capsid protein
IE: HIV-1 capsid protein
JE: HIV-1 capsid protein
KE: HIV-1 capsid protein
LE: HIV-1 capsid protein
ME: HIV-1 capsid protein
NE: HIV-1 capsid protein
OE: HIV-1 capsid protein
PE: HIV-1 capsid protein
QE: HIV-1 capsid protein
RE: HIV-1 capsid protein
SE: HIV-1 capsid protein
TE: HIV-1 capsid protein
UE: HIV-1 capsid protein
VE: HIV-1 capsid protein
WE: HIV-1 capsid protein
XE: HIV-1 capsid protein
YE: HIV-1 capsid protein
ZE: HIV-1 capsid protein
aE: HIV-1 capsid protein
bE: HIV-1 capsid protein
cE: HIV-1 capsid protein
dE: HIV-1 capsid protein
eE: HIV-1 capsid protein
fE: HIV-1 capsid protein
gE: HIV-1 capsid protein
hE: HIV-1 capsid protein
iE: HIV-1 capsid protein
jE: HIV-1 capsid protein
kE: HIV-1 capsid protein
lE: HIV-1 capsid protein
mE: HIV-1 capsid protein
nE: HIV-1 capsid protein
oE: HIV-1 capsid protein
pE: HIV-1 capsid protein
qE: HIV-1 capsid protein
rE: HIV-1 capsid protein
sE: HIV-1 capsid protein
tE: HIV-1 capsid protein
uE: HIV-1 capsid protein
vE: HIV-1 capsid protein
wE: HIV-1 capsid protein
xE: HIV-1 capsid protein
yE: HIV-1 capsid protein
zE: HIV-1 capsid protein
0E: HIV-1 capsid protein
1E: HIV-1 capsid protein
2E: HIV-1 capsid protein
3E: HIV-1 capsid protein
4E: HIV-1 capsid protein
5E: HIV-1 capsid protein
6E: HIV-1 capsid protein
7E: HIV-1 capsid protein
8E: HIV-1 capsid protein
9E: HIV-1 capsid protein
AF: HIV-1 capsid protein
BF: HIV-1 capsid protein
CF: HIV-1 capsid protein
DF: HIV-1 capsid protein
EF: HIV-1 capsid protein
FF: HIV-1 capsid protein


Theoretical massNumber of molelcules
Total (without water)9,688,301378
Polymers9,688,301378
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, TEM
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 87inner turns of helical assembly
RepresentativeModel #1minimized average structure

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Components

#1: Protein ...
HIV-1 capsid protein


Mass: 25630.426 Da / Num. of mol.: 378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: Gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P12493

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1Exp1 CORD50ms
121isotropic2Exp2 CORD500ms
131isotropic4Exp3 DARR50ms
141isotropic1Exp4 NCA
151isotropic4Exp5 NCA
161isotropic1Exp6 NCACX
171isotropic4Exp7 NCACX
181isotropic1Exp8 NCOCX
191isotropic2Exp9 NCOCX3d
1101isotropic2Exp10 CONCA3d
1111isotropic4Exp11 NCACX3d
1121isotropic4Exp12 NCOCX3d
1132isotropic1Exp13 CORD10ms
1142isotropic1Exp14 CORD20ms
1152isotropic1Exp15 CORD50ms
1162isotropic1Exp16 CORD100ms
1172isotropic1Exp17 CORD200ms
1182isotropic1Exp18 CORD300ms
1192isotropic1Exp19 CORD400ms
1202isotropic1Exp20 CORD500ms
1212isotropic2Exp21 CORD500ms
1222isotropic1Exp22 NCACX
1233isotropic3Exp23 CORD25ms
1243isotropic3Exp24 CORD500ms
1253isotropic1Exp25 CORD500ms
1263isotropic1Exp26 PAINCP
1274isotropic2Exp27 CORD25ms
1285isotropic2Exp28 R211
1295isotropic2Exp29 REDOR1ms
1305isotropic2Exp30 REDOR1.6ms
1315isotropic2Exp31 REDOR2ms
1326isotropic1Exp32 CORD50ms
1336isotropic1Exp33 PDSD1s
1347isotropic1Exp34 CORD50ms
1358isotropic2Exp35 CORD500ms
1369isotropic1Exp36 NHHC3ms
1379isotropic1Exp37 NHHC5ms

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
gel solid1100 % [U-13C; U-15N] HIV-1 capsid protein, solidU-13C,15N-CAsolid
gel solid2100 % [1,6-13C]-Glucose,U-15N HIV-1 capsid protein, solid1,6-13C-Glu,U-15N-CAsolid
gel solid3100 % [2-13C]-Glucose,U-15N HIV-1 capsid protein, solid2-13C-Glu,U-15N-CAsolid
gel solid4100 % 13C,15N-His HIV-1 capsid protein, solid13C,15N-His-CAsolid
gel solid5100 % 13C,15N-Tyr HIV-1 capsid protein, solid13C,15N-Tyr-CAsolid
gel solid650 % 13C,15N-Ala HIV-1 capsid protein, 50 % 13C,15N-Ile HIV-1 capsid, solidmixed-Ala/Ile-CAsolid
gel solid750 % 13C,15N-Ala HIV-1 capsid protein, 50 % 13C,15N-Val HIV-1 capsid, solidmixed-Ala/Val-CAsolid
gel solid886 % HIV-1 capsid protein, 14 % U-13C,15N-CA HIV-1 capsid, solidDiluted-CAsolid
gel solid950 % [U-13C] HIV-1 capsid protein, 50 % [U-15N] HIV-1 capsid, solidmixed-13C/15N-CAsolid
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 %HIV-1 capsid protein[U-13C; U-15N]1
100 %HIV-1 capsid protein[1,6-13C]-Glucose,U-15N2
100 %HIV-1 capsid protein[2-13C]-Glucose,U-15N3
100 %HIV-1 capsid protein13C,15N-His4
100 %HIV-1 capsid protein13C,15N-Tyr5
50 %HIV-1 capsid protein13C,15N-Ala6
50 %HIV-1 capsid13C,15N-Ile6
50 %HIV-1 capsid protein13C,15N-Ala7
50 %HIV-1 capsid13C,15N-Val7
86 %HIV-1 capsid proteinnatural abundance8
14 %HIV-1 capsidU-13C,15N-CA8
50 %HIV-1 capsid protein[U-13C]9
50 %HIV-1 capsid[U-15N]9
Sample conditionsIonic strength: 2.4 M / Label: tubes / pH: 6 / Pressure: 1 atm / Temperature: 277 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8501
Bruker AVANCE IIIBrukerAVANCE III6002
Bruker AVANCE IIIBrukerAVANCE III5003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
SparkyGoddarddata analysis
TALOSCornilescu, Delaglio and Baxstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NAMD2.13James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schultenstructure calculation
RefinementMethod: data-guided molecular dynamics / Software ordinal: 8
Details: Authors state that a single set of chemical shifts, distance restraints, and dihedral angle restraints was used for all chains in the CA tube structure refinement. Due to this, the ...Details: Authors state that a single set of chemical shifts, distance restraints, and dihedral angle restraints was used for all chains in the CA tube structure refinement. Due to this, the completeness of resonance assignments is not calculated correctly by the PDB validation tool. For correct assignment metrics, please refer to PDB entry 6WAP.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: inner turns of helical assembly
Conformers calculated total number: 87 / Conformers submitted total number: 1

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