[English] 日本語
Yorodumi
- PDB-1p7k: Crystal structure of an anti-ssDNA antigen-binding fragment (Fab)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1p7k
TitleCrystal structure of an anti-ssDNA antigen-binding fragment (Fab) bound to 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid (HEPES)
Components
  • antibody heavy chain FAB
  • antibody light chain FAB
KeywordsIMMUNE SYSTEM / FAB / ANTIBODY / ANTI-DNA ANTIBODY / AUTOANTIBODY / LUPUS / HEPES
Function / homology
Function and homology information


humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / immunoglobulin complex / phagocytosis, engulfment / IgG immunoglobulin complex / immunoglobulin mediated immune response ...humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / immunoglobulin complex / phagocytosis, engulfment / IgG immunoglobulin complex / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / B cell differentiation / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / adaptive immune response / defense response to bacterium / external side of plasma membrane / extracellular space / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Igk protein / Ig gamma-1 chain C region secreted form / : / Anti-myosin immunoglobulin heavy chain variable region
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSchuermann, J.P. / Henzl, M.T. / Deutscher, S.L. / Tanner, J.J.
Citation
Journal: Proteins / Year: 2004
Title: Structure of an anti-DNA fab complexed with a non-DNA ligand provides insights into cross-reactivity and molecular mimicry.
Authors: Schuermann, J.P. / Henzl, M.T. / Deutscher, S.L. / Tanner, J.J.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: CRYSTAL STRUCTURE OF AN ANTIGEN-BINDING FRAGMENT BOUND TO SINGLE-STRANDED DNA
Authors: TANNER, J.J. / KOMISSAROV, A.A. / DEUTSCHER, S.L.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: CRYSTALLIZATION AND MOLECULAR REPLACEMENT STUDIES OF A RECOMBINANT ANTIGEN-BINDING FRAGMENT COMPLEXED WITH SINGLE-STRANDED DNA
Authors: PREWITT, S.P. / KOMISSAROV, A.A. / DEUTSCHER, S.L. / TANNER, J.J.
History
DepositionMay 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: antibody light chain FAB
H: antibody heavy chain FAB
A: antibody light chain FAB
B: antibody heavy chain FAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,51837
Polymers95,5384
Non-polymers3,98033
Water13,890771
1
L: antibody light chain FAB
H: antibody heavy chain FAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,00921
Polymers47,7692
Non-polymers2,24019
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-88 kcal/mol
Surface area19260 Å2
MethodPISA
2
A: antibody light chain FAB
B: antibody heavy chain FAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,50916
Polymers47,7692
Non-polymers1,74014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-68 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.666, 156.703, 61.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11H-801-

SO4

21H-802-

SO4

-
Components

-
Antibody , 2 types, 4 molecules LAHB

#1: Antibody antibody light chain FAB


Mass: 23616.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PCOMB3/6-HIS / Production host: Escherichia coli (E. coli) / Strain (production host): DH12S / References: UniProt: Q8VCP0, UniProt: I6L978*PLUS
#2: Antibody antibody heavy chain FAB


Mass: 24153.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PCOMB3/6-HIS / Production host: Escherichia coli (E. coli) / Strain (production host): DH12S / References: UniProt: Q9JL75, UniProt: P01868*PLUS

-
Non-polymers , 6 types, 804 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 771 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: AMMONIUM SULFATE, HEPES, PEG 400, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11731
21731
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RUH3R11.54
SYNCHROTRONNSLS X8C20.9795
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEJul 27, 2000Osmic MaxFlux confocal optics
ADSC QUANTUM 42CCDApr 22, 2001NSLS X8C BEAMLINE OPTICS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorsSINGLE WAVELENGTHMx-ray1
2NSLS X8C BEAMLINE OPTICSSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
20.97951
ReflectionResolution: 1.75→48.14 Å / Num. all: 104812 / Num. obs: 98022 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 21.7
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.1 / Num. unique all: 9734 / % possible all: 94.1

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I8M

1i8m


Resolution: 1.75→48.14 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 9796 10 %RANDOM
Rwork0.197 ---
all0.201 104748 --
obs0.197 97936 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.2987 Å2 / ksol: 0.373129 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å20 Å2
2--0.75 Å20 Å2
3----1.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.75→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6500 0 249 771 7520
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d27.7
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 1.75→1.81 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.316 992 10.3 %
Rwork0.294 8668 -
obs-9734 94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMMOL3.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4MOL3.PARAMION.TOP

+
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