[English] 日本語
Yorodumi
- PDB-5gks: Crystal structure of SLE patient-derived anti-DNA antibody -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gks
TitleCrystal structure of SLE patient-derived anti-DNA antibody
Components
  • IgG2, Fab (heavy chain)
  • lambda, Fab (light chain)
KeywordsIMMUNE SYSTEM / antibody / lupus / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsArimori, T. / Sakakibara, S. / Kikutani, H. / Takagi, J.
CitationJournal: Sci Rep / Year: 2017
Title: Clonal evolution and antigen recognition of anti-nuclear antibodies in acute systemic lupus erythematosus
Authors: Sakakibara, S. / Arimori, T. / Yamashita, K. / Jinzai, H. / Motooka, D. / Nakamura, S. / Li, S. / Takeda, K. / Katayama, J. / El Hussien, M.A. / Narazaki, M. / Tanaka, T. / Standley, D.M. / ...Authors: Sakakibara, S. / Arimori, T. / Yamashita, K. / Jinzai, H. / Motooka, D. / Nakamura, S. / Li, S. / Takeda, K. / Katayama, J. / El Hussien, M.A. / Narazaki, M. / Tanaka, T. / Standley, D.M. / Takagi, J. / Kikutani, H.
History
DepositionJul 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 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 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IgG2, Fab (heavy chain)
B: lambda, Fab (light chain)
C: IgG2, Fab (heavy chain)
D: lambda, Fab (light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8816
Polymers92,6914
Non-polymers1902
Water3,495194
1
A: IgG2, Fab (heavy chain)
B: lambda, Fab (light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4413
Polymers46,3462
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-34 kcal/mol
Surface area18500 Å2
MethodPISA
2
C: IgG2, Fab (heavy chain)
D: lambda, Fab (light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4413
Polymers46,3462
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-32 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.356, 41.167, 155.996
Angle α, β, γ (deg.)90.00, 113.07, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Antibody IgG2, Fab (heavy chain)


Mass: 23397.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody lambda, Fab (light chain)


Mass: 22948.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 8000, 0.1M Phosphate-citrate (pH 4.2), 0.2M NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 52059 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rsym value: 0.083 / Net I/σ(I): 22.8
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.619 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GKR

5gkr


Resolution: 2.05→29.65 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.658 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.192 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25534 2618 5 %RANDOM
Rwork0.21745 ---
obs0.21935 49440 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.078 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å2-1.08 Å2
2---1.97 Å20 Å2
3---1.39 Å2
Refinement stepCycle: 1 / Resolution: 2.05→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6227 0 10 194 6431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026407
X-RAY DIFFRACTIONr_bond_other_d0.0020.025817
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9498749
X-RAY DIFFRACTIONr_angle_other_deg0.904313493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4625818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67324.044225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05315969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6811517
X-RAY DIFFRACTIONr_chiral_restr0.0850.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021404
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2911.0043296
X-RAY DIFFRACTIONr_mcbond_other0.2911.0043295
X-RAY DIFFRACTIONr_mcangle_it0.531.5044106
X-RAY DIFFRACTIONr_mcangle_other0.531.5044107
X-RAY DIFFRACTIONr_scbond_it0.2281.0163111
X-RAY DIFFRACTIONr_scbond_other0.2061.013104
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.3711.5054632
X-RAY DIFFRACTIONr_long_range_B_refined3.9338.1916823
X-RAY DIFFRACTIONr_long_range_B_other3.9078.0566781
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.047→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 203 -
Rwork0.267 3559 -
obs--99 %
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)
14.65390.1065-0.95072.3086-0.18791.7883-0.0441-0.2656-0.03840.0475-0.07690.08870.00210.04910.12110.03120.01180.06570.29180.02480.1494-16.965-84.97842.617
23.4442-1.76530.97444.2041-2.76353.9245-0.0082-0.62780.04830.33110.05720.2058-0.1731-0.0967-0.0490.1443-0.06030.09770.5152-0.01930.0719-16.227-88.17363.806
34.21210.8102-0.46062.85090.13731.10930.01820.2139-0.1324-0.174-0.0458-0.04740.00680.00530.02760.04610.03110.0590.2883-0.02240.1159-13.478-105.59528.381
47.05713.41130.95635.63791.76754.153-0.01371.5234-0.2518-0.63650.2202-0.3911-0.36480.2749-0.20650.26390.1110.10680.7119-0.06920.0647-14.477-109.5887.456
53.8005-2.92740.20774.7214-1.10432.9228-0.4232-0.3139-0.09930.54640.29640.21910.34040.06510.12680.18690.04830.13020.30690.01530.156114.924-102.44546.171
64.1991.2301-3.52751.4451-1.19556.52740.3206-0.30410.17580.30480.09260.0421-0.4040.0872-0.41310.14840.02860.10060.2929-0.02420.114912.746-90.78157.522
72.2480.9409-0.31324.12211.28992.5442-0.1230.1708-0.0359-0.40880.010.06030.1430.03680.1130.12150.05170.06780.2927-0.01540.1154-45.398-123.48827.37
87.089-1.9379-2.96821.91092.02725.01010.39170.72220.1095-0.3476-0.06750.0099-0.2516-0.0292-0.32430.21190.0780.07860.37320.04120.1015-44.228-112.66314.062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 116
2X-RAY DIFFRACTION2B2 - 110
3X-RAY DIFFRACTION3C2 - 116
4X-RAY DIFFRACTION4D2 - 110
5X-RAY DIFFRACTION5A117 - 212
6X-RAY DIFFRACTION6B111 - 209
7X-RAY DIFFRACTION7C117 - 213
8X-RAY DIFFRACTION8D111 - 209

+
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