[English] 日本語
Yorodumi
- PDB-8f3a: HIV-1 gp41 coiled-coil pocket IQN17 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8f3a
TitleHIV-1 gp41 coiled-coil pocket IQN17
ComponentsIQN17
KeywordsVIRAL PROTEIN / HIV-1 / gp41 / coiled-coil / pocket
Function / homologyACETIC ACID
Function and homology information
Biological speciesHIV-1 M:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsBruun, T.U.J. / Tang, S. / Fernandez, D. / Kim, P.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)DP1 AI158125 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structure-guided stabilization improves the ability of the HIV-1 gp41 hydrophobic pocket to elicit neutralizing antibodies.
Authors: Bruun, T.U.J. / Tang, S. / Erwin, G. / Deis, L. / Fernandez, D. / Kim, P.S.
History
DepositionNov 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Oct 25, 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
A: IQN17
B: IQN17
C: IQN17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5377
Polymers16,3223
Non-polymers2164
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-65 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.857, 46.962, 136.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-258-

HOH

21C-259-

HOH

31C-269-

HOH

41C-270-

HOH

-
Components

#1: Protein/peptide IQN17


Mass: 5440.537 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) HIV-1 M:B_HXB2R (virus)
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M imidazole (pH 8.0) and 35 % 2-methyl-2,4-pentanediol (MPD)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.2→16.44 Å / Num. obs: 46268 / % possible obs: 98.83 % / Redundancy: 20 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 25.1
Reflection shellResolution: 1.2→1.24 Å / Rmerge(I) obs: 0.381 / Num. unique obs: 4269 / CC1/2: 0.993

-
Processing

Software
NameVersionClassification
PHENIXv1.19refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q7C

2q7c


Resolution: 1.2→16.44 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1873 1991 4.36 %
Rwork0.1743 --
obs0.1749 45659 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→16.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 10 218 1334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0211221
X-RAY DIFFRACTIONf_angle_d1.5721637
X-RAY DIFFRACTIONf_dihedral_angle_d13.815499
X-RAY DIFFRACTIONf_chiral_restr0.09193
X-RAY DIFFRACTIONf_plane_restr0.012205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.31391210.26422787X-RAY DIFFRACTION90
1.23-1.260.27681460.21613050X-RAY DIFFRACTION98
1.26-1.30.23921410.19143100X-RAY DIFFRACTION99
1.3-1.340.20521350.15653127X-RAY DIFFRACTION99
1.34-1.390.18671460.14643095X-RAY DIFFRACTION100
1.39-1.450.19891450.1563107X-RAY DIFFRACTION99
1.45-1.510.20681390.1443080X-RAY DIFFRACTION97
1.51-1.590.17121420.14023097X-RAY DIFFRACTION99
1.59-1.690.18231450.13463164X-RAY DIFFRACTION100
1.69-1.820.17211450.14923145X-RAY DIFFRACTION100
1.82-2.010.16981430.15373164X-RAY DIFFRACTION100
2.01-2.30.16541420.14633203X-RAY DIFFRACTION100
2.3-2.890.18261440.16513220X-RAY DIFFRACTION100
2.89-16.440.19071570.2183329X-RAY DIFFRACTION99

+
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://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