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- PDB-7e1j: Crystal structure of Pr55Gag-matrix domain in complex with IP6 in... -

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Basic information

Entry
Database: PDB / ID: 7e1j
TitleCrystal structure of Pr55Gag-matrix domain in complex with IP6 in space group C121
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: 2.72 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 C121
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
C: Capsid protein p24
D: Capsid protein p24
E: Capsid protein p24
F: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,78012
Polymers79,8206
Non-polymers3,9606
Water1,24369
1
A: Capsid protein p24
B: Capsid protein p24
C: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8906
Polymers39,9103
Non-polymers1,9803
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Capsid protein p24
E: Capsid protein p24
F: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8906
Polymers39,9103
Non-polymers1,9803
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.182, 67.414, 97.499
Angle α, β, γ (deg.)90.000, 123.150, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13303.257 Da / Num. of mol.: 6
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.: 6 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.53 %
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: 2.72→48.75 Å / Num. obs: 25978 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.041 / Rrim(I) all: 0.107 / Net I/σ(I): 14.3 / Num. measured all: 177762 / Scaling rejects: 4
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
2.72-2.856.90.8022388134380.8810.3270.8672.499.9
9.02-48.756.40.03748547540.9990.0150.0444.699.1

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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: 2.72→44.414 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2723 1306 5.03 %
Rwork0.213 24651 -
obs0.2159 25957 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.83 Å2 / Biso mean: 67.9589 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.72→44.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5290 0 324 69 5683
Biso mean--143.69 54.86 -
Num. residues----665
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.7201-2.8290.36031310.31432732
2.829-2.95770.31391700.27282698
2.9577-3.11360.2791280.25122711
3.1136-3.30860.34251690.26142686
3.3086-3.56390.29751440.23432743
3.5639-3.92240.27611630.20072728
3.9224-4.48950.25271600.18022743
4.4895-5.65450.23551060.19172781
5.6545-44.40.23891350.19862829
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)
10.04110.0483-0.16720.26860.25150.5518-0.07030.34140.17030.1017-0.31170.53550.4998-0.4569-0.00590.59250.0435-0.02330.5170.02460.552432.068113.581853.9086
20.79910.0374-0.43850.18170.13180.5850.04930.72540.1782-0.27160.17970.1827-0.0744-0.29920.01180.65720.1042-0.03340.39290.11130.450841.477912.914543.0467
30.2474-0.0959-0.17860.13220.1010.1433-0.1657-0.129-0.264-0.7368-0.2832-0.11721.31850.4108-0.00420.53010.08970.00010.4460.06340.422942.67876.20258.499
40.02410.0183-0.1160.1805-0.05090.5974-0.1538-0.97120.08760.67850.044-0.1283-0.1084-0.24570.00010.48790.1201-0.09770.5189-0.08740.531144.372517.080564.2851
50.3450.07020.26770.3111-0.40760.5254-0.092-0.45280.5345-0.21230.1719-0.1969-0.14550.2545-0.00040.56040.0482-0.0080.4228-0.02250.55148.866916.028255.8334
61.5339-0.0690.25890.0574-0.01540.0486-0.23860.60950.169-0.23020.00760.2329-0.31180.02570.01440.62910.0465-0.04870.36290.09960.845637.637724.713449.7443
70.5986-0.441-0.30140.69740.22540.0942-0.1917-0.13921.8195-0.51530.51290.4304-0.11180.54140.06630.61640.01340.12770.64580.13410.886647.698325.761350.9445
80.4720.05050.49350.42150.01780.72570.0449-0.15910.1848-1.01410.26980.3918-0.1563-0.87140.00931.223-0.0242-0.24281.2467-0.12631.193552.72335.69759.976
90.51730.3579-0.06510.31980.15860.1436-0.55530.0122-0.7450.34870.152-0.22560.42570.4698-0.00950.49360.1096-0.04820.57230.00650.448250.7807-4.79692.1104
100.8731-1.3183-0.53582.0050.61651.0794-0.73760.6039-0.83910.92930.4911.37090.637-0.5409-0.11010.38050.0662-0.03580.45820.11190.415338.61243.326890.0752
110.16070.1823-0.10310.3306-0.1910.04430.14610.9561-0.9272-0.24730.1323-0.4876-0.23380.12040.00280.58620.0720.03550.5154-0.06270.476650.0433-2.423879.0291
120.12850.1485-0.3060.2992-0.26031.06710.1762-0.09950.2654-0.2949-0.7972-0.80630.19981.5469-0.04390.47890.06030.02130.7110.01340.454158.43986.560481.9679
130.41910.0712-0.39630.0478-0.08640.45420.0067-0.26460.2107-0.0852-0.19810.090.0172-0.594-00.42410.0253-0.08030.56320.0240.359849.14978.982682.0969
140.0203-0.04070.06370.3807-0.33420.28310.0738-0.6469-0.76960.30070.720.7226-0.7397-0.4797-0.00990.8520.1052-0.06770.6598-0.03320.521747.8318.478196.9669
150.2407-0.04990.14140.08560.10630.2424-0.3473-0.68580.6610.4142-0.06560.0181-0.7601-0.1030.00670.80450.0687-0.06450.5402-0.08880.646748.091415.650390.4301
168.30282.00055.64061.99978.10023.8326-0.26820.3425-0.1888-0.77810.384-0.6227-1.17050.2623-0.35241.53-0.00190.21131.23040.37141.228954.696119.220485.8689
170.1642-0.0695-0.18270.26690.16870.2735-0.34390.2908-0.01970.32770.34470.13320.09030.10170.00070.45090.07110.20980.5391-0.00710.516574.8904-4.383551.93
180.2110.0445-0.06280.01120.02330.0383-0.0101-0.046-0.21930.40210.2485-0.50060.20680.4971-0.01220.52310.1249-0.0050.61230.00080.575778.4023-8.408365.2425
190.0252-0.1017-0.06970.16650.09360.1178-0.0963-0.6721-0.6721-0.60.53860.8881-0.0609-0.1973-0.00150.48130.1149-0.03020.52280.03850.584763.88-2.99559.6265
200.1367-0.14570.23530.5896-0.02180.27180.54530.53090.2129-0.471-0.053-0.2439-0.7363-0.62360.00120.5190.0920.13350.50970.06150.549567.32159.143859.3042
210.4261-0.3217-0.08610.24280.24220.2340.0014-0.6891-0.31220.16460.2114-0.262-0.32520.2651-0.0020.46080.02350.07160.59730.03350.513970.56713.942666.6815
220.8353-0.67580.38640.82670.41012.637-0.1752-0.77541.0421-0.18551.4909-0.3021.29980.89750.08640.4819-0.16210.02490.7918-0.13040.6784.42511.431560.9062
230.4044-0.42480.17260.5084-0.07940.1973-0.3016-1.0430.17781.42250.4151-0.9551-0.74820.52960.02680.6732-0.073-0.02220.6817-0.11210.560281.37687.002468.2456
240.0274-0.21090.40370.4966-0.80661.3518-0.86671.0113-0.52370.28870.2295-0.471-0.84370.156-0.05591.0684-0.43850.17441.6506-0.43691.709481.50516.79868.488
25-0.01310.01910.09250.30450.19250.0138-0.0881-0.5479-0.50870.3912-0.1348-0.08180.3927-0.0071-0.00140.49860.0493-0.04930.52040.05320.399827.70224.37950.6192
260.65920.005-0.0450.16720.50071.4911-0.7760.4571-0.1576-0.94870.9698-0.6603-0.66231.9170.02370.4736-0.06910.11030.4294-0.01690.449333.0254.413737.2594
271.360.23990.53450.01270.08260.2077-0.2999-0.58281.2315-0.09150.16930.0112-0.3814-0.0833-0.01180.38740.0743-0.03870.22610.01350.454718.410210.673942.8883
280.47810.377-0.41790.4568-0.05390.4716-0.2475-0.1344-0.16320.153-0.09620.33530.233-0.7404-0.00010.44360.02260.01740.48990.04940.511212.6885-0.731943.3018
290.6111-0.40530.29190.3761-0.00720.15490.09610.15080.0469-0.4482-0.0818-0.26470.4157-0.1172-00.46890.07030.00550.45730.08840.420318.6740.789735.4495
300.15420.07080.09970.15810.00380.05860.6010.0856-0.27150.8312-0.4536-0.924-0.63760.4457-0.04090.55490.0719-0.16370.38130.11480.637830.6752-6.735441.9817
310.04280.0217-0.08460.26740.05320.21680.1688-0.1515-0.6257-0.1773-0.0831-0.85570.02920.47430.00390.3882-0.0185-0.03080.46430.03610.587824.0434-8.419334.7791
320.325-0.3779-0.12530.44540.13070.0934-0.12370.25810.1111-0.07810.03590.3078-0.1572-0.455-0.00311.0308-0.0639-0.41420.99620.0041.274215.6079-12.415533.946
330.1705-0.2098-0.15860.4064-0.05880.9617-0.1234-0.3464-0.2320.16760.52160.6517-0.693-0.13270.02360.35560.03560.03170.48990.02480.7042-16.719318.627449.3243
340.05480.15130.12860.16330.13220.1004-0.6077-0.8379-0.04461.57150.57660.2393-0.2876-0.30350.00060.75680.13510.09770.60730.09580.6766-8.871913.568459.0367
350.0338-0.1362-0.03210.26610.088-0.0011-0.4517-0.2851-0.07250.1017-0.16120.101-0.2362-0.4447-0.0010.42680.02740.00080.42580.05720.501-3.190817.984743.9458
360.0808-0.07380.10960.2875-0.24010.31470.34740.6828-0.4592-0.6983-0.32210.83520.2585-0.362-0.00010.3101-0.0126-0.02490.4474-0.06210.6361-9.20229.094237.7807
370.3390.0847-0.1860.44330.3120.3456-0.0528-0.5238-0.45910.35040.0230.38730.4026-0.03390.00110.397-0.0180.05430.3560.01150.5801-5.57746.69246.4089
381.4515-1.03431.00411.64150.73733.3094-0.97120.2089-0.23670.4256-0.43830.32190.046-0.205-0.53070.5947-0.19670.20810.79070.28090.9737-18.83417.102453.9787
390.52120.5768-0.11340.5746-0.15760.024-0.3082-0.9331-0.7838-0.38830.350.60670.7455-0.1833-0.03730.6780.06310.20260.5243-0.03210.8794-13.11110.173451.5307
400.0584-0.08720.20130.124-0.33381.1572-0.04440.36690.1764-0.3080.0796-0.06490.30120.06640.00441.38060.00440.30931.15560.07851.7359-15.4949-7.116244.8852
410.13180.1507-0.13390.15960.03270.3289-0.33280.87520.2813-0.10560.0530.40170.44650.5053-0.00230.63880.11140.0520.50280.09810.363610.637119.53769.1656
420.5401-0.06370.0340.6744-0.01960.05050.51371.32290.4815-0.39110.0503-0.06580.2808-0.39130.04190.40120.015-0.02530.5740.06620.3294-1.582124.570911.9938
430.1023-0.1712-0.12190.40220.10580.0462-0.414-0.31270.27540.38620.213-0.4071-0.7997-0.23430.00150.48750.1501-0.07420.46690.00760.33918.877818.891624.3291
440.51260.2058-0.51150.773-0.11541.0249-0.0669-0.2312-0.9874-0.434-0.2497-0.71490.86650.8132-0.06890.61690.1118-0.00340.4357-0.03210.33968.03737.035420.3745
450.1910.2727-0.00930.586-0.46530.7004-0.29530.1278-0.0648-0.199-0.29720.52960.539-1.1725-0.00060.4339-0.0481-0.03060.4789-0.13390.4023-0.058612.031220.1718
461.1107-0.4982-0.48220.76560.66310.54260.2068-0.12870.3177-0.8133-0.22580.30460.5725-0.38310.27250.9743-0.4215-0.82420.2036-1.2075-2.0236-0.165113.94444.9719
470.33330.1348-0.56420.046-0.220.99090.03110.8475-0.2897-0.64270.28440.3092-0.2232-0.30870.23150.6429-0.0869-0.17040.4759-0.22120.4708-5.49869.246410.6261
480.1277-0.06820.06060.2799-0.09830.0032-0.1918-1.20180.4723-0.0621-0.2047-0.0345-0.2308-0.0403-0.00951.07550.1312-0.13951.3223-0.181.471-4.995-4.4448.803
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 17 )A0 - 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 115 )A107 - 122
9X-RAY DIFFRACTION9chain 'B' and (resid -1 through 17 )B-1 - 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 107 )B107 - 122
17X-RAY DIFFRACTION17chain 'C' and (resid -1 through 17 )C-1 - 17
18X-RAY DIFFRACTION18chain 'C' and (resid 18 through 30 )C18 - 30
19X-RAY DIFFRACTION19chain 'C' and (resid 31 through 42 )C31 - 42
20X-RAY DIFFRACTION20chain 'C' and (resid 43 through 64 )C43 - 64
21X-RAY DIFFRACTION21chain 'C' and (resid 65 through 89 )C65 - 89
22X-RAY DIFFRACTION22chain 'C' and (resid 90 through 95 )C90 - 95
23X-RAY DIFFRACTION23chain 'C' and (resid 96 through 106 )C96 - 106
24X-RAY DIFFRACTION24chain 'C' and (resid 107 through 109 )C107 - 122
25X-RAY DIFFRACTION25chain 'D' and (resid -1 through 17 )D-1 - 17
26X-RAY DIFFRACTION26chain 'D' and (resid 18 through 30 )D18 - 30
27X-RAY DIFFRACTION27chain 'D' and (resid 31 through 42 )D31 - 42
28X-RAY DIFFRACTION28chain 'D' and (resid 43 through 64 )D43 - 64
29X-RAY DIFFRACTION29chain 'D' and (resid 65 through 89 )D65 - 89
30X-RAY DIFFRACTION30chain 'D' and (resid 90 through 95 )D90 - 95
31X-RAY DIFFRACTION31chain 'D' and (resid 96 through 106 )D96 - 106
32X-RAY DIFFRACTION32chain 'D' and (resid 107 through 108 )D107 - 122
33X-RAY DIFFRACTION33chain 'E' and (resid 3 through 17 )E3 - 17
34X-RAY DIFFRACTION34chain 'E' and (resid 18 through 30 )E18 - 30
35X-RAY DIFFRACTION35chain 'E' and (resid 31 through 42 )E31 - 42
36X-RAY DIFFRACTION36chain 'E' and (resid 43 through 64 )E43 - 64
37X-RAY DIFFRACTION37chain 'E' and (resid 65 through 89 )E65 - 89
38X-RAY DIFFRACTION38chain 'E' and (resid 90 through 95 )E90 - 95
39X-RAY DIFFRACTION39chain 'E' and (resid 96 through 106 )E96 - 106
40X-RAY DIFFRACTION40chain 'E' and (resid 107 through 110 )E107 - 122
41X-RAY DIFFRACTION41chain 'F' and (resid 2 through 17 )F2 - 17
42X-RAY DIFFRACTION42chain 'F' and (resid 18 through 30 )F18 - 30
43X-RAY DIFFRACTION43chain 'F' and (resid 31 through 42 )F31 - 42
44X-RAY DIFFRACTION44chain 'F' and (resid 43 through 64 )F43 - 64
45X-RAY DIFFRACTION45chain 'F' and (resid 65 through 89 )F65 - 89
46X-RAY DIFFRACTION46chain 'F' and (resid 90 through 95 )F90 - 95
47X-RAY DIFFRACTION47chain 'F' and (resid 96 through 106 )F96 - 106
48X-RAY DIFFRACTION48chain 'F' and (resid 107 through 112 )F107 - 122

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