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- PDB-7tbp: X-ray structure of the HIV-1 myristoylated matrix protein -

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Basic information

Entry
Database: PDB / ID: 7tbp
TitleX-ray structure of the HIV-1 myristoylated matrix protein
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN / HIV-1 / matrix / Gag / myristoyl group
Function / homology
Function and homology information


viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / structural molecule activity / RNA binding / cytoplasm
Similarity search - Function
: / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal
Similarity search - Domain/homology
CITRIC ACID / MYRISTIC ACID / Gag protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å
AuthorsGreen, T.J. / Saad, J.S. / Samal, A.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)9R01AI150901 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Atomic view of the HIV-1 matrix lattice; implications on virus assembly and envelope incorporation.
Authors: Samal, A.B. / Green, T.J. / Saad, J.S.
History
DepositionDec 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,9718
Polymers37,8823
Non-polymers1,0895
Water1,51384
1
B: Capsid protein p24
hetero molecules

B: Capsid protein p24
hetero molecules

B: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,85912
Polymers37,8823
Non-polymers1,9769
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
2
A: Capsid protein p24
hetero molecules

A: Capsid protein p24
hetero molecules

A: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1739
Polymers37,8823
Non-polymers1,2916
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
3
C: Capsid protein p24

C: Capsid protein p24

C: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)37,8823
Polymers37,8823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)96.562, 96.562, 216.908
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-325-

HOH

21A-327-

HOH

31A-329-

HOH

41A-331-

HOH

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Components

#1: Protein Capsid protein p24 / Matrix protein p17 / Nucleocapsid protein p7


Mass: 12627.417 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Plasmid: pET-19B / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus RIL-competent cells / References: UniProt: C1JB69
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 40% PEG 400, 0.1 M Bis-Tris-propane buffer (pH 4.7)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97954 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 2.15→24.9 Å / Num. obs: 21434 / % possible obs: 99.61 % / Redundancy: 6.1 % / Biso Wilson estimate: 43.01 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04682 / Rpim(I) all: 0.02045 / Rrim(I) all: 0.05124 / Net I/σ(I): 21.66
Reflection shellResolution: 2.15→2.228 Å / Rmerge(I) obs: 0.5734 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 2087 / CC1/2: 0.805 / CC star: 0.945 / Rpim(I) all: 0.2634 / Rrim(I) all: 0.6327 / % possible all: 98.86

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HIW

1hiw


Resolution: 2.151→24.896 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 1996 9.31 %
Rwork0.1843 19433 -
obs0.1872 21429 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.68 Å2 / Biso mean: 66.2679 Å2 / Biso min: 26.93 Å2
Refinement stepCycle: final / Resolution: 2.151→24.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 58 84 2641
Biso mean--96.12 60.51 -
Num. residues----310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062589
X-RAY DIFFRACTIONf_angle_d0.7973463
X-RAY DIFFRACTIONf_chiral_restr0.048372
X-RAY DIFFRACTIONf_plane_restr0.005443
X-RAY DIFFRACTIONf_dihedral_angle_d15.5341596
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1513-2.20510.32731380.2687134398
2.2051-2.26470.32631290.23931377100
2.2647-2.33130.26761500.22371358100
2.3313-2.40650.2931430.21181398100
2.4065-2.49240.24351410.19041361100
2.4924-2.59210.23831420.19391378100
2.5921-2.70990.24831500.1851368100
2.7099-2.85260.24271450.1911387100
2.8526-3.03110.25461390.1981390100
3.0311-3.26460.2811400.20151394100
3.2646-3.59230.25071450.1961388100
3.5923-4.11010.21371400.16481412100
4.1101-5.17060.21061420.15331422100
5.1706-24.8960.22231520.1703145798
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)
17.88726.2-5.86664.9995-4.73195.1779-0.28011.31230.172-1.8482-0.0075-0.625-0.1666-0.49420.25540.7669-0.05580.08190.8444-0.08010.6691-18.937949.31274.302
23.2621-3.0917-3.54813.46843.57784.3054-0.1198-1.2751-0.0940.66430.4716-0.6826-0.27690.5567-0.44230.3053-0.04130.01220.4188-0.02140.3664-20.549539.60877.5684
33.16-0.7172-1.26957.957-3.50413.18540.35810.6793-1.1671-1.19750.0354-1.04842.80881.7684-0.33270.76170.2387-0.01570.5778-0.08750.6417-19.591928.25546.0547
41.47881.9291-3.07257.4284-1.83416.9222-0.8972.1378-0.0119-0.65570.82430.92870.3756-1.49570.08140.3829-0.1349-0.0430.55650.06720.3679-35.443234.02063.4973
52.37022.78111.43736.91363.14515.71060.34040.29620.84190.0564-0.37441.1733-0.56950.01940.1540.2908-0.0416-0.02610.36320.05380.6689-38.908339.500511.0976
66.06143.86380.1174.85391.53394.02070.2604-0.6605-0.14371.0387-0.42620.7810.4334-0.24320.19780.4174-0.0310.12440.42040.01040.3966-37.633230.880218.3132
75.58413.17251.8674.4084.36138.5111-0.05730.0612-0.5250.3014-0.13520.13350.58020.04930.02410.31460.01140.00940.29550.0170.2848-30.957831.073212.9541
83.4293-2.0791-2.8063.87464.35715.1424-0.0653-1.3190.71160.68250.5047-1.3448-0.35771.8558-0.58310.4318-0.0017-0.10920.5895-0.05640.621-19.923736.75417.1334
97.29711.7419-5.03485.0495-0.00726.434-0.4576-1.6225-0.07172.51430.5666-0.66410.53561.51170.6250.95670.12890.01080.5630.20040.352-25.14429.647122.3041
107.26385.0592-4.16816.55770.97677.3596-0.01020.01630.9362-0.22190.3328-0.0895-0.5039-0.1923-0.10060.48120.0889-0.03610.4443-0.07020.712-22.750817.731628.8511
114.00622.7655-1.52163.87631.93469.90320.3051-0.5299-1.9655-0.2734-0.10480.91431.4778-1.7741-0.28530.5962-0.1048-0.10560.65170.07680.8353-27.31994.691730.0634
125.3308-3.1247-4.97673.00423.08994.719-0.4307-1.3485-0.61720.73190.5337-0.69350.17430.6084-0.10340.51360.1399-0.06990.6366-0.00030.4868-10.94758.573532.2302
134.24631.46933.1339.4026-4.26346.8855-0.00320.87110.957-0.0504-0.5639-0.8181-0.24340.26910.33890.3589-0.0030.07040.3612-0.05640.661-6.932513.274124.7132
146.7198-3.94131.29322.8298-1.52613.61090.33170.4736-0.0676-1.2309-0.2518-0.02770.2385-0.1693-0.08940.53640.04570.03470.47430.05290.3395-10.07495.061717.7239
156.0075-5.15881.35934.6038-2.29964.0911-0.06850.3362-0.2762-0.9765-0.13730.14450.5746-0.39280.21180.43240.034-0.02170.3707-0.01040.4155-16.28566.317323.0942
168.05293.6538-2.25288.5062-4.38186.30610.99631.2841-0.6888-0.9651-1.03121.40080.21870.49-0.23630.45880.0822-0.19420.6985-0.04590.6538-26.631913.450319.4237
173.72851.1668-4.03343.5378-2.36655.3493-0.62651.8149-1.0227-2.29280.030.43111.3042-1.41520.2681.0248-0.0619-0.15870.7382-0.220.7596-22.31875.939714.4039
181.34192.6135-2.51657.3978-6.06995.3474-1.38020.88040.1728-0.8627-1.4521-0.98371.72531.42061.0251.15060.3356-0.24480.9472-0.20551.35549.691427.24648.2016
199.4671-1.4568-3.43037.13190.5097.1685-0.1311.0684-1.58520.35760.27471.26452.1978-1.31240.04531.0059-0.0379-0.14810.705-0.04181.4868-2.663427.96727.2064
203.3219-3.4418-1.18994.60873.33646.12870.41760.87150.8784-0.6899-0.48020.2596-0.4313-0.41050.02860.44570.1243-0.00130.640.21990.89287.243844.13048.577
214.4714-6.2207-2.04979.55032.09176.9739-0.5802-1.6934-0.5850.8330.2840.55150.43830.1050.23250.49650.05670.01490.6250.0180.70432.312444.62220.1664
225.3908-4.93020.72635.49311.98218.4518-0.0241-0.4645-0.38090.2668-0.38030.38820.3857-0.66620.35850.521-0.0395-0.04780.47420.17670.85331.764838.126214.5155
230.081-0.0006-0.74960.0222-0.00467.2793-0.05310.8611-1.94750.99430.05962.38030.66891.64460.27571.1157-0.0382-0.01580.62340.08141.64956.459726.74417.4582
242.77963.82211.50016.0244.72732.02650.3223-1.6365-1.94180.99630.76480.91421.69510.43160.19530.99230.07260.34271.28050.56631.5307-0.35531.236722.6923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 11 )B3 - 11
2X-RAY DIFFRACTION2chain 'B' and (resid 12 through 18 )B12 - 18
3X-RAY DIFFRACTION3chain 'B' and (resid 19 through 30 )B19 - 30
4X-RAY DIFFRACTION4chain 'B' and (resid 31 through 43 )B31 - 43
5X-RAY DIFFRACTION5chain 'B' and (resid 44 through 53 )B44 - 53
6X-RAY DIFFRACTION6chain 'B' and (resid 54 through 72 )B54 - 72
7X-RAY DIFFRACTION7chain 'B' and (resid 73 through 89 )B73 - 89
8X-RAY DIFFRACTION8chain 'B' and (resid 90 through 96 )B90 - 96
9X-RAY DIFFRACTION9chain 'B' and (resid 97 through 109 )B97 - 109
10X-RAY DIFFRACTION10chain 'A' and (resid 6 through 18 )A6 - 18
11X-RAY DIFFRACTION11chain 'A' and (resid 19 through 30 )A19 - 30
12X-RAY DIFFRACTION12chain 'A' and (resid 31 through 43 )A31 - 43
13X-RAY DIFFRACTION13chain 'A' and (resid 44 through 53 )A44 - 53
14X-RAY DIFFRACTION14chain 'A' and (resid 54 through 72 )A54 - 72
15X-RAY DIFFRACTION15chain 'A' and (resid 73 through 89 )A73 - 89
16X-RAY DIFFRACTION16chain 'A' and (resid 90 through 96 )A90 - 96
17X-RAY DIFFRACTION17chain 'A' and (resid 97 through 108 )A97 - 108
18X-RAY DIFFRACTION18chain 'C' and (resid 10 through 18 )C10 - 18
19X-RAY DIFFRACTION19chain 'C' and (resid 19 through 30 )C19 - 30
20X-RAY DIFFRACTION20chain 'C' and (resid 31 through 53 )C31 - 53
21X-RAY DIFFRACTION21chain 'C' and (resid 54 through 72 )C54 - 72
22X-RAY DIFFRACTION22chain 'C' and (resid 73 through 89 )C73 - 89
23X-RAY DIFFRACTION23chain 'C' and (resid 90 through 96 )C90 - 96
24X-RAY DIFFRACTION24chain 'C' and (resid 97 through 107 )C97 - 107

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