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- PDB-7e1k: Crystal structure of Pr55Gag-matrix domain in complex with IP6 in... -

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Basic information

Entry
Database: PDB / ID: 7e1k
TitleCrystal structure of Pr55Gag-matrix domain in complex with IP6 in space group R32
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN / HIV-1 / Matrix protein / Myo-inositol hexakisphosphate / Serial femtosecond X-ray crystallography / Ambient-temperature crystallography
Function / homology
Function and homology information


viral process / viral nucleocapsid / host cell cytoplasm / 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) / 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
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Gag protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsDeMirci, H. / Senda, T. / Destan, E.
Funding support United States, Turkey, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-1231306 United States
Other government118C270 Turkey
CitationJournal: To Be Published
Title: Crystal structure of Pr55Gag-matrix domain in complex with IP6 in space group R32
Authors: DeMirci, H. / Senda, T. / Destan, E.
History
DepositionFeb 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Capsid protein p24
B: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7194
Polymers27,3992
Non-polymers1,3202
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-2 kcal/mol
Surface area14770 Å2
Unit cell
Length a, b, c (Å)97.828, 97.828, 176.297
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 13699.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: T2CJ20
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3350 and 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 2, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→48.91 Å / Num. obs: 12979 / % possible obs: 99.9 % / Redundancy: 20.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.049 / Rrim(I) all: 0.222 / Net I/σ(I): 12 / Num. measured all: 263912
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.4921.21.7072813313290.860.3791.7492.2100
8.98-48.9117.70.042496328010.010.04440.998.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
PHENIXDEV-3318refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→39.1 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2759 621 4.8 %
Rwork0.2203 12310 -
obs0.2233 12931 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.88 Å2 / Biso mean: 51.1964 Å2 / Biso min: 18.71 Å2
Refinement stepCycle: final / Resolution: 2.4→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 126 97 2124
Biso mean--124.71 57.44 -
Num. residues----242
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4002-2.64170.33931490.25443027100
2.6417-3.02390.27661530.24953051100
3.0239-3.80930.26461370.21293080100
3.8093-390.26851820.2063315299
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)
10.0354-0.1273-0.31360.21110.19280.70730.02750.4988-0.238-0.1332-0.3038-0.4939-0.4790.3191-0.0090.220.04730.08550.3827-0.03260.5083-24.170673.15921.6768
20.68120.0891-0.38120.15240.23670.7198-0.68280.6895-0.6542-0.60760.8066-0.10280.7182-0.49480.02760.42960.00610.05320.26970.05780.484-32.754862.615321.4904
30.6844-0.18720.20370.82030.42490.17960.05820.372-0.525-0.71780.00130.66810.16060.15060.03050.393-0.01280.0410.3401-0.00720.2786-36.879578.33718.9487
40.7397-0.6851-0.52380.8690.27150.55190.4532-0.1990.42020.2276-0.253-0.0926-0.56360.48090.01160.29330.02390.01730.223-0.03010.4136-35.006181.877230.7974
50.4334-0.4159-0.05940.8769-0.31440.07530.1087-0.2473-0.46420.21070.01730.13710.0869-0.1459-00.23590.009-0.02530.2639-0.02430.2396-38.856973.020229.4561
60.50070.358-0.19890.29130.02491.8872-0.1572-0.20470.3130.0168-0.2726-0.93910.82890.3852-0.05450.2840.1003-0.09090.3834-0.07360.4723-26.350165.40432.34
70.1834-0.04040.23450.0244-0.04340.27360.2404-0.00930.14340.12420.0388-0.09130.09220.5220.02480.29020.04320.07320.3114-0.04220.2489-33.756266.21337.1825
80.7755-0.4939-0.28390.4899-0.00340.2173-0.1942-0.00630.01330.26320.0218-0.3450.37880.311-0.00390.5949-0.05740.02580.59730.08430.6246-31.419474.520353.6288
91.0021-0.2060.09120.0825-0.24370.7467-0.023-0.268-0.9260.46630.37941.21460.533-0.05680.04770.4453-0.02460.04190.38550.11580.5631-50.812656.782268.4095
100.75840.32890.35550.41930.29240.86970.0085-1.41980.0072-0.27790.23760.52530.64220.54770.0390.33250.0380.01790.3712-0.02130.2791-37.683159.53268.9464
111.5405-0.83940.59550.7407-0.49320.2827-0.4422-0.45570.40250.12720.0156-0.4334-0.1177-0.1471-0.08570.37520.0335-0.04510.2969-0.0410.2259-49.327970.841971.2255
120.4476-0.00650.16720.3608-0.2530.45080.00430.0540.2963-0.00560.00120.8079-0.0380.04460.00150.3093-0.0128-0.04840.32490.00250.323-53.213571.175859.4386
130.40940.1046-0.28810.2894-0.00920.0777-0.11030.09210.3541-0.22240.1454-0.13820.1217-0.0532-0.00040.3673-0.0113-0.02160.2448-0.040.3272-43.652370.169660.854
140.5792-0.3597-0.14760.3176-0.16290.69240.4429-0.3388-0.2222-0.2659-0.58970.37760.73110.14340.01670.72310.13450.10240.3002-0.05980.5615-43.1455.498658.0751
150.15530.09310.18330.03150.16890.33230.4517-0.072-0.09970.17810.50870.10.4915-0.21520.0050.44320.01960.05170.3768-0.00120.3173-40.098462.393153.3492
160.4058-0.3825-0.10920.40.13030.0784-0.0830.1291.28340.34060.01990.04661.05961.16870.00560.57470.0055-0.0250.49940.2870.509-48.918864.777137.0279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 17 )A2 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 30 )A18 - 30
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 42 )A31 - 42
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 64 )A43 - 64
5X-RAY DIFFRACTION5chain 'A' and (resid 65 through 89 )A65 - 89
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 95 )A90 - 95
7X-RAY DIFFRACTION7chain 'A' and (resid 96 through 106 )A96 - 106
8X-RAY DIFFRACTION8chain 'A' and (resid 107 through 121 )A107 - 122
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 17 )B2 - 17
10X-RAY DIFFRACTION10chain 'B' and (resid 18 through 30 )B18 - 30
11X-RAY DIFFRACTION11chain 'B' and (resid 31 through 42 )B31 - 42
12X-RAY DIFFRACTION12chain 'B' and (resid 43 through 64 )B43 - 64
13X-RAY DIFFRACTION13chain 'B' and (resid 65 through 89 )B65 - 89
14X-RAY DIFFRACTION14chain 'B' and (resid 90 through 95 )B90 - 95
15X-RAY DIFFRACTION15chain 'B' and (resid 96 through 106 )B96 - 106
16X-RAY DIFFRACTION16chain 'B' and (resid 107 through 122 )B107 - 122

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