[English] 日本語
Yorodumi
- PDB-4m0i: CRYSTAL STRUCTURE OF SYNTHETIC HIV-1 CAPSID C-TERMINAL DOMAIN (CT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m0i
TitleCRYSTAL STRUCTURE OF SYNTHETIC HIV-1 CAPSID C-TERMINAL DOMAIN (CTD) C198S mutant
ComponentsHIV-1 CAPSID PROTEIN
KeywordsVIRAL PROTEIN / HIV-1 CAPSID / CORE PROTEIN / HIV-1 CAPSID C-TERMINAL DOMAIN / AIDS
Function / homology
Function and homology information


viral process / viral capsid
Similarity search - Function
Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHowell, K. / Tolbert, W.D. / Pazgier, M. / Lu, W.
CitationJournal: To be Published
Title: Molecular basis of disulfide bonding-regulated HIV-1 capsid assembly
Authors: Howell, K. / Li, C. / Tolbert, W.D. / Beckett, D. / Pazgier, M. / Lu, W.
History
DepositionAug 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,5151
Polymers9,5151
Non-polymers00
Water362
1
A: HIV-1 CAPSID PROTEIN

A: HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)19,0302
Polymers19,0302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area1430 Å2
ΔGint-13 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.001, 59.001, 61.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein HIV-1 CAPSID PROTEIN


Mass: 9514.855 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, residues 146-231 / Mutation: C198S / Source method: obtained synthetically
Details: This sequence is the HIV-1 CAPSID C-TERMINAL DOMAIN with the cysteine 198 to serine mutation
Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q71B91
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 M ammonium sulfate, 100 mM sodium cacodylate pH 6.5, and 200 mM sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9753 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 4, 2013 / Details: RH COATED FLAT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9753 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 2648 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 30.7
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2.2 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LRY

3lry


Resolution: 2.8→30.61 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 25.209 / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.086 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29379 117 4.5 %RANDOM
Rwork0.236 ---
all0.23893 2508 --
obs0.23893 2486 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 94.951 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å2-0 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms565 0 0 2 567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02574
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.979775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.755570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.51925.18527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.8915108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.233154
X-RAY DIFFRACTIONr_chiral_restr0.0780.287
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021428
X-RAY DIFFRACTIONr_mcbond_it7.3929.225283
X-RAY DIFFRACTIONr_mcangle_it11.63113.83352
X-RAY DIFFRACTIONr_scbond_it8.4359.636291
X-RAY DIFFRACTIONr_long_range_B_refined17.887.1572357
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.526 9 -
Rwork0.404 184 -
obs--99.48 %

+
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