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- PDB-7rao: Structure of M66I mutant of disulfide stabilized HIV-1 CA hexamer -

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Basic information

Entry
Database: PDB / ID: 7rao
TitleStructure of M66I mutant of disulfide stabilized HIV-1 CA hexamer
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN
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 / structural molecule activity / virion membrane / 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
IODIDE ION / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsBester, S.M. / Kvaratskhelia, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI157802 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32-AI150547 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54-AI150472 United States
CitationJournal: To Be Published
Title: Structural and mechanistic bases of viral resistance to long-acting HIV-1 capsid inhibitor, Lenacapavir
Authors: Bester, S.M. / Annamalai, A.S. / Adu-Ampratwum, D. / Haney, R. / Fuchs, J.R. / Kvaratskhelia, M.
History
DepositionJul 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein p24
B: Capsid protein p24
C: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,02425
Polymers76,3303
Non-polymers1,69422
Water6,792377
1
A: Capsid protein p24
B: Capsid protein p24
hetero molecules

A: Capsid protein p24
B: Capsid protein p24
hetero molecules

A: Capsid protein p24
B: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,68845
Polymers152,6596
Non-polymers3,02939
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
2
C: Capsid protein p24
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)156,76960
Polymers152,6596
Non-polymers4,10954
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Unit cell
Length a, b, c (Å)158.962, 158.962, 57.711
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 6 or resid 8...
d_2ens_1(chain "B" and (resid 1 through 6 or resid 8...
d_3ens_1(chain "C" and (resid 1 through 6 or resid 8...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROLEUA1 - 6
d_12ens_1GLYLYSA8 - 131
d_13ens_1TRPILEA134 - 154
d_14ens_1GLNPHEA156 - 162
d_15ens_1ASPALAA164 - 175
d_16ens_1GLNGLNA177
d_17ens_1LEUVALA190 - 192
d_18ens_1ASNLEUA194 - 212
d_19ens_1GLUGLNA214 - 220
d_21ens_1PROLEUB1 - 6
d_22ens_1GLYLYSB8 - 131
d_23ens_1TRPILEB133 - 153
d_24ens_1GLNPHEB155 - 161
d_25ens_1ASPALAB163 - 174
d_26ens_1GLNGLNB176
d_27ens_1LEUVALB180 - 182
d_28ens_1ASNLEUB184 - 202
d_29ens_1GLUGLNB204 - 210
d_31ens_1PROLEUC1 - 6
d_32ens_1GLYLYSC8 - 131
d_33ens_1TRPILEC133 - 153
d_34ens_1GLNPHEC155 - 161
d_35ens_1ASPALAC163 - 174
d_36ens_1GLNGLNC176
d_37ens_1LEUVALC182 - 184
d_38ens_1ASNLEUC186 - 204
d_39ens_1GLUGLNC206 - 212

NCS oper:
IDCodeMatrixVector
1given(-0.999955155955, -0.00517892896368, -0.0079287309317), (0.00521354474177, -0.999976941694, -0.00435144025911), (-0.0079060123086, -0.00439258191638, 0.99995909926)158.603308917, -92.2681140491, 0.447680593907
2given(0.0247637030091, -0.999689957498, 0.00259767043647), (-0.999685580285, -0.0247736605519, -0.00387379838332), (0.0039369511468, -0.00250092408499, -0.999989122838)-47.7416631291, 78.3481427387, 26.638633275

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Components

#1: Protein Capsid protein p24 / CA


Mass: 25443.234 Da / Num. of mol.: 3 / Mutation: A14C, E45C, M66I, W184A, M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12493
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.125-0.35M Sodium Iodide, 2-8% Peg 3350, 6% glycerol, 0.1M sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.29→44.23 Å / Num. obs: 37715 / % possible obs: 99.7 % / Redundancy: 2 % / Biso Wilson estimate: 31.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.2
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 2 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 2 / Num. unique obs: 3732 / CC1/2: 0.921 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3h47
Resolution: 2.29→44.22 Å / SU ML: 0.2752 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5375
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2436 1898 5.04 %
Rwork0.2155 35781 -
obs0.2169 37679 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.81 Å2
Refinement stepCycle: LAST / Resolution: 2.29→44.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 22 377 5379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00175101
X-RAY DIFFRACTIONf_angle_d0.46866936
X-RAY DIFFRACTIONf_chiral_restr0.0389784
X-RAY DIFFRACTIONf_plane_restr0.0041905
X-RAY DIFFRACTIONf_dihedral_angle_d15.74991931
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.636929385386
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.611229363572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.350.31151160.27632545X-RAY DIFFRACTION98.96
2.35-2.410.29421470.23272554X-RAY DIFFRACTION100
2.41-2.480.2711270.23512530X-RAY DIFFRACTION99.85
2.48-2.560.27861420.23862518X-RAY DIFFRACTION99.96
2.56-2.650.26651510.23392538X-RAY DIFFRACTION100
2.65-2.760.27121460.22052550X-RAY DIFFRACTION99.81
2.76-2.880.25091620.23322505X-RAY DIFFRACTION99.96
2.89-3.040.26781330.21982553X-RAY DIFFRACTION99.96
3.04-3.230.25641220.21582577X-RAY DIFFRACTION100
3.23-3.480.22091350.20932554X-RAY DIFFRACTION100
3.48-3.830.24751260.21232534X-RAY DIFFRACTION97.79
3.83-4.380.22771050.17692597X-RAY DIFFRACTION99.37
4.38-5.520.21091500.19292576X-RAY DIFFRACTION99.93
5.52-44.220.21641360.2352650X-RAY DIFFRACTION99.08
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.35989043797-0.9590193902422.776131536751.74036601769-1.539593531717.841736176170.05969096776960.0333569670097-0.367772631583-0.07650727279640.0832209051633-0.136155631740.5460316371130.956932897027-0.07643806163370.2278306114650.02470333463980.03201874763970.3269462455280.004927956357230.29746398897827.8598004825-22.983210565228.5301128762
21.15646922661.32960016598-1.641707058421.78565521957-2.749599926764.66501324365-0.22891547979-0.7719539056980.08824741243490.4743886446050.121330485720.3850337765240.4228707568760.4429984093040.0005008407381040.5117125893240.1548609095130.0414886819990.5486925425460.0531024464430.28316108367423.3375250789-25.85422435147.2865900871
32.14365041602-0.138517533319-0.8785899671012.10808210476-1.929087451614.617194422-0.0686048479334-0.388270578983-0.129446163870.241857059063-0.0449099550139-0.0409830159898-0.2535467367670.2735623610180.0993959468860.187250485245-0.0110170776919-0.01007015372480.203047463003-0.02604700010510.21673563377322.1032569976-16.52552747234.8825018826
43.078392687592.25782831458-1.376136373485.76131617085-3.524472451675.46958056297-0.2739744573810.2540980099-0.390957707177-0.9267400104860.08696833082570.3850944537050.780733361844-0.2421419879890.1710955220340.306744252597-0.04463536619310.01811137263390.319415464441-0.02586191684390.30040854916234.16571339142.284794500388.49565734274
50.862469245725-1.399394912291.324838615433.96074460904-4.715393263267.4928042499-0.347784951833-0.166643308626-0.2100980682581.20425328559-0.0605958387349-0.7093263700470.4899968871981.536533055660.3299718713230.6105520673650.067402072447-0.0798221071350.514266521211-0.1075003436630.32684538320642.55229883482.8276526066214.662122953
62.897434240621.13370908135-2.534561353384.790941692843.599786803668.04766325511-0.3060935207820.0986640693187-0.179110597116-0.5003590457660.3153798720480.168015660805-0.4388411008780.8182468626270.05028140429270.287826450284-0.08391962294610.01173965933730.365015177012-0.01012692039810.36730020338541.477145651114.45565505110.1432793708
71.248269539180.152259169055-0.1297142788232.59873126941-0.2967082553841.26877130692-0.03076361433860.0341258119906-0.0405635821555-0.14247420994-0.03020920184410.09501553883950.0466003636633-0.0837909561270.04655750729320.181456041936-0.0240349489687-0.002418575506610.1886858397480.007871723482970.216518780793.559209413-62.7484632516-1.53495765048
82.57765893555-0.384388090362-0.7197202802252.3619350295-1.32963510014.633650077520.1646953568440.420335597087-0.0226054126306-0.608518207107-0.121492635339-0.07597964798030.3357246659740.1639900461020.02328458919560.335563804018-0.007457241725030.03790661765080.278759606291-0.01622248007080.29524605980699.3460693229-67.8945540267-11.477151746
94.59547925415-0.03007072272030.1821742284414.00235067488-0.2501324838094.16793758211-0.00923480237055-0.195040159722-0.2389549136430.1450418688270.01486378790870.1226617643120.3190073077720.06136217389020.03153246065050.2677437776880.00929670663612-0.0135377197260.1568426142210.01025243792940.27172588685276.3955410873-83.892784628616.4661817509
106.795420677192.750248881730.9685231881495.83098747733-4.464263202459.074930237910.0360774410002-0.171086021613-0.0827720755621-1.492813333420.8470230371460.3123876607640.403444776672-0.320271149753-0.647967820310.320339180575-0.03691556364140.05597483778850.3405273157260.04342700009440.45518381530364.6818282091-85.215924944912.4823386823
111.586101450050.3059371567871.255509899583.011227503120.4074374012562.32457484281-0.04622597084760.0943162736183-0.142796476234-0.2637271085590.0521494745296-0.23402926779-0.1450985808110.0897655548616-0.04569198360390.2066707533270.01326826749820.02781643176580.332746156620.02977232294640.3120274396971.393838899-33.4220227194-2.11532109383
120.636893841146-0.1100152716830.1059143481241.32064897842-0.04712486143562.25812657985-0.0253552514337-0.03896918914720.0332691072541-0.1499009069960.009566677620240.211746614594-0.11702740485-0.0786896250150.01927526179230.197909842426-0.0275948621548-0.01189237311020.255179695601-0.03066973463450.25517036347559.0105910534-24.3871505284-1.20788143884
130.7420403244621.234477466082.121153798152.156134076353.66915599546.118069332840.3080398918540.4924189378060.0365334693781-0.724642602417-0.508190254580.231469861969-0.390332698485-0.209048142060.2602756089240.5362311785310.117505114295-0.09163221034990.575544641455-4.87779160267E-50.34171758678153.0390414719-23.2119318275-20.1635248013
143.363739741010.2162031813360.7094991293414.492271993120.3158820849352.903716223520.08275578968530.350469071811-0.0345767516649-0.338299075921-0.01695377096010.4664363327570.0006760701449380.50012641954-0.02046577162590.3667492496770.0139465393837-0.051845312940.338423823671-0.06905681117030.29772769164460.1531706183-29.0471852188-16.5850229339
152.026309197640.6629575731152.527970580382.224389337572.402580461169.5332849337-0.05601058679450.03818873623230.305188492854-0.239884038892-0.179770171683-0.0703835740821-0.701329822136-0.1943373661970.2836817878890.217967554801-0.00363741006105-0.01557834097980.1797122133020.01041303873710.30356588133564.5213944253-19.842203860.48928543676
165.44717188956-0.1564489203130.9253656969543.52902048490.3386487335962.51510083268-0.236955217838-0.6045854118550.2115734778030.355647564976-0.07171101260970.1101699119160.02921142091-0.1334668780330.2502325802040.266758233104-0.01488548221770.006642200989020.388392016446-0.03543767046220.25841212484479.7191013501-10.201228569422.6355296799
175.945441900072.050812334872.747344898082.069232535970.6198347932824.408316324970.232331889749-0.116749759793-0.582276191218-0.184225657588-0.03823323718380.04233568314290.09046908605980.137242942156-0.1686176401560.2674100144050.0163254055477-0.0291340421740.2140610913430.02476500633660.28280625202481.8649290066-13.476681388915.6329251115
186.967799153893.072089588492.529031620175.689439728361.42659825282.66154441761-0.5733468540070.2397416798790.796349483186-0.8110224839070.00720192552847-0.209701310876-1.02406524797-0.3039709433060.4322309387730.3873472746580.074379156236-0.0148140981770.320834184459-0.05925259880690.39756743693682.8741019211-4.216046381315.9311077768
195.00024428812-0.215825205835-1.764936519026.038748867944.464629819063.81648548247-0.0255782034569-0.1357639870850.01312756238-0.3412716265440.363472949636-0.689710119533-0.5685918251820.44624104876-0.4031093407630.371629458814-0.0632261825094-0.03371133472660.38310677091-0.01176341576260.58416030586793.9385671451-4.3986187423216.7654327543
205.90420386843-0.628059686581.615423121325.98907777974-2.316753061111.83908945967-0.100727648704-0.7137375712390.5129297103760.307742178434-0.2864045517080.368806467722-0.558100302612-0.1435773794670.387322460.3657845631210.02065776468340.01036575981660.433903034039-0.09449538841970.3706046566938.51527303675-7.823088351142.6598805849
211.47309088256-0.481620068219-0.394797082951.39848751647-0.5021242127830.6942223672330.08356033463110.1020331824410.02338771130830.00930559979950.006007369311820.0712117606257-0.04344570223960.0978461648952-0.08088848934730.201789124774-0.00247531327517-0.01398346375450.171245675873-0.01357398778340.21137726260814.9509420092-10.875299840523.9796772178
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 63 through 83 )CC63 - 8363 - 83
22chain 'C' and (resid 84 through 104 )CC84 - 10484 - 104
33chain 'C' and (resid 105 through 145 )CC105 - 145105 - 145
44chain 'C' and (resid 146 through 175 )CC146 - 175146 - 175
55chain 'C' and (resid 176 through 192 )CC176 - 192176 - 185
66chain 'C' and (resid 193 through 220 )CC193 - 220186 - 213
77chain 'A' and (resid 1 through 83 )AA1 - 831 - 83
88chain 'A' and (resid 84 through 145 )AA84 - 14584 - 146
99chain 'A' and (resid 146 through 205 )AA146 - 205147 - 206
1010chain 'A' and (resid 206 through 219 )AA206 - 219207 - 220
1111chain 'B' and (resid 1 through 43 )BB1 - 431 - 43
1212chain 'B' and (resid 44 through 83 )BB44 - 8344 - 83
1313chain 'B' and (resid 84 through 104 )BB84 - 10484 - 104
1414chain 'B' and (resid 105 through 125 )BB105 - 125105 - 125
1515chain 'B' and (resid 126 through 145 )BB126 - 145126 - 145
1616chain 'B' and (resid 146 through 160 )BB146 - 160146 - 160
1717chain 'B' and (resid 161 through 175 )BB161 - 175161 - 175
1818chain 'B' and (resid 176 through 195 )BB176 - 195176 - 186
1919chain 'B' and (resid 196 through 220 )BB196 - 220187 - 211
2020chain 'C' and (resid 1 through 16 )CC1 - 161 - 16
2121chain 'C' and (resid 17 through 62 )CC17 - 6217 - 62

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