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- PDB-7jxs: Crystal Structure Human Immunodeficiency Virus-1 Matrix protein M... -

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Basic information

Entry
Database: PDB / ID: 7jxs
TitleCrystal Structure Human Immunodeficiency Virus-1 Matrix protein Mutant Q63R Crystal Form 2
ComponentsMatrix protein
KeywordsSTRUCTURAL PROTEIN / HIV-1 / gag
Function / homologyviral process / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / structural molecule activity / ACETATE ION / Gag protein
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsGreen, T.J. / Eastep, G.N. / Ghanam, R.H. / Saad, J.S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)9R01AI150901 United States
Other government1S10RR026478 United States
Other governmentP30 CA013148 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural characterization of HIV-1 matrix mutants implicated in envelope incorporation.
Authors: Eastep, G.N. / Ghanam, R.H. / Green, T.J. / Saad, J.S.
History
DepositionAug 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix protein
B: Matrix protein
C: Matrix protein
D: Matrix protein
E: Matrix protein
F: Matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,50020
Polymers93,5556
Non-polymers1,94514
Water1,20767
1
A: Matrix protein
C: Matrix protein
E: Matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,86410
Polymers46,7783
Non-polymers1,0867
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Matrix protein
D: Matrix protein
F: Matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,63610
Polymers46,7783
Non-polymers8597
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.548, 90.724, 73.169
Angle α, β, γ (deg.)90.000, 102.390, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 7 through 109)
21(chain B and resid 7 through 109)
31(chain C and resid 7 through 109)
41chain D
51(chain E and resid 7 through 109)
61(chain F and resid 7 through 109)
12chain H
22chain I
32chain J

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 7 through 109)A7 - 109
211(chain B and resid 7 through 109)B7 - 109
311(chain C and resid 7 through 109)C7 - 109
411chain DD7 - 109
511(chain E and resid 7 through 109)E7 - 109
611(chain F and resid 7 through 109)F7 - 109
112chain HH1
212chain II1
312chain JJ1

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Matrix protein


Mass: 15592.562 Da / Num. of mol.: 6 / Mutation: Q63R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): codon-plus RIL-competent cells / References: UniProt: Q6E183

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Non-polymers , 5 types, 81 molecules

#2: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4
Details: 40 % PEG 400, 0.1 M NaAcetate (pH 4.0), 0.05 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→45.36 Å / Num. obs: 32585 / % possible obs: 94.51 % / Redundancy: 3.1 % / CC1/2: 0.987 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.05 / Rrim(I) all: 0.088 / Net I/σ(I): 25.95
Reflection shellResolution: 2.35→2.434 Å / Rmerge(I) obs: 0.431 / Num. unique obs: 3286 / CC1/2: 0.807 / Rpim(I) all: 0.277 / Rrim(I) all: 0.515 / % possible all: 95.36

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HIW

1hiw


Resolution: 2.35→45.36 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 2000 6.14 %
Rwork0.216 30585 -
obs0.2184 32585 94.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.24 Å2 / Biso mean: 65.7491 Å2 / Biso min: 33.79 Å2
Refinement stepCycle: final / Resolution: 2.35→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5111 0 108 67 5286
Biso mean--64.19 61.45 -
Num. residues----632
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3164X-RAY DIFFRACTION16.468TORSIONAL
12B3164X-RAY DIFFRACTION16.468TORSIONAL
13C3164X-RAY DIFFRACTION16.468TORSIONAL
14D3164X-RAY DIFFRACTION16.468TORSIONAL
15E3164X-RAY DIFFRACTION16.468TORSIONAL
16F3164X-RAY DIFFRACTION16.468TORSIONAL
21A0X-RAY DIFFRACTION16.468TORSIONAL
22B0X-RAY DIFFRACTION16.468TORSIONAL
23C0X-RAY DIFFRACTION16.468TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.410.29261370.24212086222390
2.41-2.470.27531480.23382271241998
2.47-2.540.27011470.2212251239897
2.54-2.630.27291420.2232178232095
2.63-2.720.26691510.22122297244899
2.72-2.830.28821480.22662269241799
2.83-2.960.29581460.23192243238998
2.96-3.110.28831490.2372279242898
3.11-3.310.28371490.23062272242198
3.31-3.560.23921440.22492203234795
3.56-3.920.25671340.2092048218288
3.92-4.490.23651300.20161987211785
4.49-5.650.28461270.21131948207584
5.65-45.360.20431480.20332253240195
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1222-1.6561-1.10045.11.5561.58750.1589-0.43830.4044-0.32040.1715-0.6749-0.48041.09160.00580.5132-0.05490.05620.5093-0.04760.783537.0388-5.544513.3613
25.81212.92853.38622.5778-0.24954.365-0.0028-1.35631.99930.37480.20060.4529-0.6849-1.1432-0.03130.47550.10960.00260.4850.03620.568522.3219-2.749414.9484
38.7649-9.16162.05639.58741.83831.9344-1.4957-1.25162.00710.90070.6834-0.1107-1.2874-0.924-0.87680.3383-0.0880.0730.62090.28950.557319.5972-10.756819.9965
43.38533.2367-0.01195.80411.52063.54480.1271-0.1595-0.8873-0.14850.0351-0.07190.7515-0.47940.00090.62440.00950.07320.46160.05880.73120.1164-17.167610.695
55.40980.2118-1.34664.65624.10083.93290.2530.5486-0.2575-1.2035-0.109-0.1010.48290.263-00.4420.00040.04690.23670.0240.459226.7321-11.6510.461
62.07480.07996.48841.3840.73084.37510.44481.4684-0.74130.4243-0.629-0.3597-0.28920.71.29380.55610.24150.04640.4242-0.01280.847738.6041-15.790214.3363
71.0867-0.8420.09461.85420.7211.61690.03250.8587-0.7339-0.12410.1272-1.67521.33860.16990.32880.70290.01980.01210.5461-0.04670.738632.7977-21.59768.0218
82.27053.43950.29955.4066-0.28024.3896-0.33720.9012-0.3667-0.99810.35550.26350.3692-0.5564-0.01190.6761-0.0238-0.01480.3686-0.02480.413818.23148.4621-4.0049
92.7889-1.9061.15750.82350.83553.0969-0.2326-0.9577-0.19020.46840.1095-0.14520.2721-0.2441-0.03220.4552-0.00170.0360.3736-0.0490.468616.15348.723211.9246
102.0665-0.2091-0.83411.7227-1.15192.9046-0.2988-0.79971.45050.02030.30520.1525-1.0366-0.29150.0060.5528-0.0272-0.01190.4468-0.13640.670722.679219.939212.3318
112.18352.51680.41223.06491.48787.54240.40440.1852-0.0892-0.40320.036-0.61160.42280.95970.210.4182-0.0325-0.04340.2234-0.01310.475322.036414.39825.7981
122.0746-3.55020.70733.26830.46861.27440.17582.20690.4536-1.29710.14190.4623-0.5397-0.8142-0.1520.7742-0.01030.02870.5897-0.01630.783817.272118.6644-5.5892
130.0361-0.8489-0.00064.40950.09690.0282-0.12590.39530.8136-1.2650.4352-0.5615-0.7905-0.04210.02050.8322-0.1420.08730.81510.02630.94924.233925.77710.5319
141.4344-0.00950.3851.04591.12021.39630.0041.6321-0.2086-0.81-0.31610.6556-0.0233-0.1647-0.020.8917-0.162-0.26590.83180.1270.7737-1.7014-4.5123-16.8155
154.36170.19512.9163.49990.72911.6637-0.3418-0.530.59030.1950.0825-0.01560.01540.0410.01660.5923-0.11530.01190.4610.03680.49529.5139-4.4775-4.9861
163.92740.1484-2.77292.0994-1.22922.2727-0.7903-0.7963-1.6923-0.2228-0.0519-0.60160.45811.0476-0.20670.6074-0.09190.00420.49750.10880.50065.6096-16.0373-1.221
175.701-1.05221.60081.9533-3.32686.5691-0.13230.7448-0.4097-0.23010.04610.94060.8633-1.57090.01910.8153-0.2962-0.02440.61140.00150.65070.8794-11.9141-10.3866
180.0911-0.92520.65772.1899-0.9822-0.18630.31431.0197-0.9498-0.721-0.03230.07940.30530.5260.00560.8065-0.1477-0.10920.7853-0.0930.9763-1.3113-24.9363-10.2265
196.76990.3339-1.76185.8798-0.27858.71320.0626-0.6835-0.58440.11710.18290.38360.690.22390.00230.51460.0595-0.05930.6764-0.04980.499512.990710.829739.7692
202.76182.23030.89443.3223-1.70366.3314-0.1749-0.11341.1679-0.1718-0.1170.0799-2.61161.09250.00390.6889-0.028-0.02020.8235-0.17030.749818.795421.542830.4751
212.34231.5697-1.37685.6924-3.20372.08760.19910.08680.5038-0.5081-0.67320.9673-1.1552-2.2123-0.41590.50550.11030.00080.8939-0.32320.559910.95518.237337.6473
221.66972.0443-0.37553.71040.63870.78680.1722-0.98982.2057-0.7104-0.27072.5672-1.7976-0.73780.10760.98410.1069-0.04020.9313-0.13680.87897.210426.764735.4277
236.554-0.14210.10694.7262-0.80759.3143-0.1573-0.21030.21680.11990.04340.1367-0.189-0.9485-0.00610.5266-0.02760.0080.72590.07020.5604-4.4102-8.703122.463
243.8956-2.996-0.73031.73370.76024.75590.587-1.5310.16790.3693-0.2482-0.64530.22290.40890.09130.402-0.0720.0480.68080.12810.50551.7-12.989322.8088
256.10732.14394.17278.11515.48698.42142.1782-2.3729-3.24693.567-0.55641.38873.5673-0.91541.24920.6782-0.2787-0.18111.03020.45410.7014-5.2248-21.19328.7352
263.44663.27651.15213.70280.34171.59020.3922-0.3895-0.31770.2394-0.2233-0.32160.23560.39690.00010.49060.0103-0.03340.9926-0.11750.577846.03067.976526.1979
271.02550.44531.08412.9191-0.98833.07750.169-0.6790.7220.04870.04740.4882-1.0987-0.4762-0.0010.6472-0.0196-0.03880.9596-0.27310.650836.816420.01424.3183
284.7477-1.86792.81653.79821.8894.77420.442-1.57560.15380.3254-0.2898-0.1762-0.6880.76790.02020.5069-0.0355-0.01811.0249-0.21330.701946.295615.653427.8421
292.83842.40251.49526.38240.54220.7820.594-0.7074-0.44720.6728-0.6343-0.4225-0.1421-2.0512-0.24330.48520.12620.01811.3812-0.34750.337547.559225.918929.8564
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 30 )A7 - 30
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 43 )A31 - 43
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 53 )A44 - 53
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 72 )A54 - 72
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 89 )A73 - 89
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 96 )A90 - 96
7X-RAY DIFFRACTION7chain 'A' and (resid 97 through 110 )A97 - 110
8X-RAY DIFFRACTION8chain 'B' and (resid 7 through 30 )B7 - 30
9X-RAY DIFFRACTION9chain 'B' and (resid 31 through 53 )B31 - 53
10X-RAY DIFFRACTION10chain 'B' and (resid 54 through 72 )B54 - 72
11X-RAY DIFFRACTION11chain 'B' and (resid 73 through 89 )B73 - 89
12X-RAY DIFFRACTION12chain 'B' and (resid 90 through 96 )B90 - 96
13X-RAY DIFFRACTION13chain 'B' and (resid 97 through 112 )B97 - 112
14X-RAY DIFFRACTION14chain 'C' and (resid 7 through 30 )C7 - 30
15X-RAY DIFFRACTION15chain 'C' and (resid 31 through 53 )C31 - 53
16X-RAY DIFFRACTION16chain 'C' and (resid 54 through 72 )C54 - 72
17X-RAY DIFFRACTION17chain 'C' and (resid 73 through 96 )C73 - 96
18X-RAY DIFFRACTION18chain 'C' and (resid 97 through 116 )C97 - 116
19X-RAY DIFFRACTION19chain 'D' and (resid 7 through 53 )D7 - 53
20X-RAY DIFFRACTION20chain 'D' and (resid 54 through 72 )D54 - 72
21X-RAY DIFFRACTION21chain 'D' and (resid 73 through 96 )D73 - 96
22X-RAY DIFFRACTION22chain 'D' and (resid 97 through 109 )D97 - 109
23X-RAY DIFFRACTION23chain 'E' and (resid 7 through 67 )E7 - 67
24X-RAY DIFFRACTION24chain 'E' and (resid 68 through 89 )E68 - 89
25X-RAY DIFFRACTION25chain 'E' and (resid 90 through 110 )E90 - 110
26X-RAY DIFFRACTION26chain 'F' and (resid 7 through 53 )F7 - 53
27X-RAY DIFFRACTION27chain 'F' and (resid 54 through 72 )F54 - 72
28X-RAY DIFFRACTION28chain 'F' and (resid 73 through 96 )F73 - 96
29X-RAY DIFFRACTION29chain 'F' and (resid 97 through 111 )F97 - 111

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