[English] 日本語
Yorodumi
- PDB-6u9u: Structure of GM9_TH8seq732127 FAB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6u9u
TitleStructure of GM9_TH8seq732127 FAB
Components(GM9_TH8seq732127 FAB ...) x 2
KeywordsIMMUNE SYSTEM / Fragment binding antigen
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / FORMIC ACID
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsSingh, S. / Liban, T.J. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P01 AI104722 United States
CitationJournal: J.Exp.Med. / Year: 2020
Title: Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses.
Authors: Phad, G.E. / Pushparaj, P. / Tran, K. / Dubrovskaya, V. / Adori, M. / Martinez-Murillo, P. / Vazquez Bernat, N. / Singh, S. / Dionne, G. / O'Dell, S. / Bhullar, K. / Narang, S. / Sorini, C. ...Authors: Phad, G.E. / Pushparaj, P. / Tran, K. / Dubrovskaya, V. / Adori, M. / Martinez-Murillo, P. / Vazquez Bernat, N. / Singh, S. / Dionne, G. / O'Dell, S. / Bhullar, K. / Narang, S. / Sorini, C. / Villablanca, E.J. / Sundling, C. / Murrell, B. / Mascola, J.R. / Shapiro, L. / Pancera, M. / Martin, M. / Corcoran, M. / Wyatt, R.T. / Karlsson Hedestam, G.B.
History
DepositionSep 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: GM9_TH8seq732127 FAB heavy chain
L: GM9_TH8seq732127 FAB light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,63512
Polymers47,2812
Non-polymers35410
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-81 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.709, 147.709, 63.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11H-434-

HOH

-
Components

-
Antibody , 2 types, 2 molecules HL

#1: Antibody GM9_TH8seq732127 FAB heavy chain


Mass: 24084.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody GM9_TH8seq732127 FAB light chain


Mass: 23196.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Non-polymers , 4 types, 136 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 4M Sodium Formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 33355 / % possible obs: 100 % / Redundancy: 17.9 % / Biso Wilson estimate: 47.66 Å2 / CC1/2: 0.999 / Net I/σ(I): 27.8
Reflection shellResolution: 2.26→2.3 Å / Num. unique obs: 1625 / CC1/2: 0.837

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→16.783 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.99
RfactorNum. reflection% reflection
Rfree0.2495 1582 4.77 %
Rwork0.2081 --
obs0.2102 33193 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 251.1 Å2 / Biso mean: 71.8684 Å2 / Biso min: 22.65 Å2
Refinement stepCycle: final / Resolution: 2.26→16.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 36 126 3416
Biso mean--86.39 57.43 -
Num. residues----430
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.26-2.33210.32271420.2809279499
2.3321-2.41520.2641330.2712819100
2.4152-2.51160.29531370.26182848100
2.5116-2.62550.32171340.2732846100
2.6255-2.76330.28351540.25842843100
2.7633-2.93560.30691430.25622821100
2.9356-3.16090.31391440.25662884100
3.1609-3.47640.2421510.22282858100
3.4764-3.97360.25961580.19552892100
3.9736-4.98450.17371330.1492942100
4.9845-16.780.23031530.18823064100
Refinement TLS params.Method: refined / Origin x: -47.2537 Å / Origin y: -11.3864 Å / Origin z: -4.0669 Å
111213212223313233
T0.3538 Å20.2013 Å20.0424 Å2-0.4254 Å20.1771 Å2--0.3142 Å2
L0.3254 °2-0.1654 °2-0.0121 °2-0.2662 °20.3028 °2--0.3344 °2
S-0.1165 Å °-0.061 Å °0.0426 Å °0.0744 Å °-0.0457 Å °-0.0244 Å °0.2405 Å °0.5883 Å °-0.0624 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH1 - 224
2X-RAY DIFFRACTION1allL1 - 212
3X-RAY DIFFRACTION1allB1 - 6
4X-RAY DIFFRACTION1allF1
5X-RAY DIFFRACTION1allF2
6X-RAY DIFFRACTION1allE1
7X-RAY DIFFRACTION1allE2
8X-RAY DIFFRACTION1allS1 - 131

+
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