[English] 日本語
Yorodumi
- PDB-4jha: Crystal Structure of RSV-Neutralizing Human Antibody D25 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jha
TitleCrystal Structure of RSV-Neutralizing Human Antibody D25
Components
  • D25 antigen-binding fragment heavy chain
  • D25 light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / Ig
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMclellan, J.S. / Chen, M. / Leung, S. / Graepel, K.W. / Du, X. / Yang, Y. / Zhou, T. / Baxa, U. / Yasuda, E. / Beaumont, T. ...Mclellan, J.S. / Chen, M. / Leung, S. / Graepel, K.W. / Du, X. / Yang, Y. / Zhou, T. / Baxa, U. / Yasuda, E. / Beaumont, T. / Kumar, A. / Modjarrad, K. / Zheng, Z. / Zhao, M. / Xia, N. / Kwong, P.D. / Graham, B.S.
CitationJournal: Science / Year: 2013
Title: Structure of RSV fusion glycoprotein trimer bound to a prefusion-specific neutralizing antibody.
Authors: McLellan, J.S. / Chen, M. / Leung, S. / Graepel, K.W. / Du, X. / Yang, Y. / Zhou, T. / Baxa, U. / Yasuda, E. / Beaumont, T. / Kumar, A. / Modjarrad, K. / Zheng, Z. / Zhao, M. / Xia, N. / ...Authors: McLellan, J.S. / Chen, M. / Leung, S. / Graepel, K.W. / Du, X. / Yang, Y. / Zhou, T. / Baxa, U. / Yasuda, E. / Beaumont, T. / Kumar, A. / Modjarrad, K. / Zheng, Z. / Zhao, M. / Xia, N. / Kwong, P.D. / Graham, B.S.
History
DepositionMar 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: D25 antigen-binding fragment heavy chain
L: D25 light chain


Theoretical massNumber of molelcules
Total (without water)47,8302
Polymers47,8302
Non-polymers00
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-27 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.725, 108.725, 139.909
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11H-311-

HOH

21H-396-

HOH

31H-414-

HOH

41L-303-

HOH

51L-399-

HOH

61L-402-

HOH

-
Components

#1: Antibody D25 antigen-binding fragment heavy chain


Mass: 24504.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293 / Production host: homo sapiens (human)
#2: Antibody D25 light chain


Mass: 23325.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293 / Production host: homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / pH: 4.6
Details: 22% (w/v) PEG 4000, 0.1 M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 21, 2012
RadiationMonochromator: SI 220. ROSENBAUM-ROCK DOUBLE- CRYSTAL MONOCHROMATOR:
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 63455 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 11 %
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.3 % / % possible all: 86.1

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GBM, 3IDX

3gbm

3idx


Resolution: 1.6→35.4 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 26.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 3211 5.07 %
Rwork0.24 --
obs0.241 63360 98.1 %
all-64653 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→35.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3302 0 0 270 3572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073387
X-RAY DIFFRACTIONf_angle_d1.1974617
X-RAY DIFFRACTIONf_dihedral_angle_d12.591211
X-RAY DIFFRACTIONf_chiral_restr0.087535
X-RAY DIFFRACTIONf_plane_restr0.006591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6009-1.62480.31491440.29382097X-RAY DIFFRACTION81
1.6248-1.65020.27161020.28062324X-RAY DIFFRACTION88
1.6502-1.67730.26961340.27292421X-RAY DIFFRACTION93
1.6773-1.70620.28121280.27952540X-RAY DIFFRACTION96
1.7062-1.73720.28871360.26082581X-RAY DIFFRACTION98
1.7372-1.77060.2831500.24282603X-RAY DIFFRACTION100
1.7706-1.80680.27531470.2412628X-RAY DIFFRACTION100
1.8068-1.8460.22861350.23612634X-RAY DIFFRACTION100
1.846-1.8890.26191390.24092619X-RAY DIFFRACTION100
1.889-1.93620.26631210.24412653X-RAY DIFFRACTION100
1.9362-1.98860.29111330.24912649X-RAY DIFFRACTION100
1.9886-2.04710.23571280.23612653X-RAY DIFFRACTION100
2.0471-2.11310.2591320.23832665X-RAY DIFFRACTION100
2.1131-2.18870.24951490.2352642X-RAY DIFFRACTION100
2.1887-2.27630.25321430.23472655X-RAY DIFFRACTION100
2.2763-2.37990.23981420.24162652X-RAY DIFFRACTION100
2.3799-2.50530.27951330.25982682X-RAY DIFFRACTION100
2.5053-2.66220.25691500.24852671X-RAY DIFFRACTION100
2.6622-2.86770.24071250.24642713X-RAY DIFFRACTION100
2.8677-3.15610.29971660.24042678X-RAY DIFFRACTION100
3.1561-3.61240.241530.23572730X-RAY DIFFRACTION100
3.6124-4.54970.23951490.21162763X-RAY DIFFRACTION100
4.5497-35.40470.24291720.25292896X-RAY DIFFRACTION99
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)
12.91330.0418-0.21621.4215-0.21861.05020.00980.0710.06080.11290.00290.13680.0499-0.05860.02560.1541-0.03080.01850.1596-0.02590.1402-6.388628.7258-14.7487
21.3180.74051.20151.31050.57232.59450.0542-0.72640.12892.48290.3656-2.03450.61330.26180.20261.42040.1542-0.69790.5674-0.18640.794219.307426.02984.1949
34.52871.85891.56754.43031.36721.9053-0.0104-0.22330.11060.2077-0.02960.01-0.1982-0.06350.05290.1813-0.00640.02140.1423-0.02580.1479-0.811450.2208-10.411
43.7012-1.85911.71130.3302-0.41551.1445-0.0006-0.09810.1010.1422-0.0843-0.62910.39610.58110.01110.84190.0743-0.37180.5745-0.12691.278931.460735.1373-0.087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN H AND RESID 1:114 )
2X-RAY DIFFRACTION2(CHAIN H AND RESID 115:213 )
3X-RAY DIFFRACTION3(CHAIN L AND RESID 1:114 )
4X-RAY DIFFRACTION4(CHAIN L AND RESID 115:211 )

+
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