[English] 日本語
Yorodumi
- PDB-7tbp: X-ray structure of the HIV-1 myristoylated matrix protein -

+
Open data


ID or keywords:

Loading...

-
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 process / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / RNA binding / cytoplasm
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, N-terminal / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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)

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more