[English] 日本語
Yorodumi
- PDB-1fj1: LYME DISEASE ANTIGEN OSPA IN COMPLEX WITH NEUTRALIZING ANTIBODY F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fj1
TitleLYME DISEASE ANTIGEN OSPA IN COMPLEX WITH NEUTRALIZING ANTIBODY FAB LA-2
Components
  • HYBRIDOMA ANTIBODY LA2 (HEAVY CHAIN)
  • HYBRIDOMA ANTIBODY LA2 (LIGHT CHAIN)
  • OUTER SURFACE PROTEIN A
KeywordsIMMUNE SYSTEM / OSPA / LYME DISEASE / ANTIBODY FAB FRAGMENT / NEUTRALIZING EPITOPE
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / immunoglobulin mediated immune response / complement activation, classical pathway / positive regulation of phagocytosis / antigen binding / B cell differentiation / cell outer membrane / positive regulation of immune response / antibacterial humoral response / cell surface / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
C1 set domains (antibody constant domain-like) / Outer Surface Protein A; domain 3 - #1 / Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / Outer Surface Protein A; domain 3 / : / Lipocalin / : / Prokaryotic membrane lipoprotein lipid attachment site profile. ...C1 set domains (antibody constant domain-like) / Outer Surface Protein A; domain 3 - #1 / Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / Outer Surface Protein A; domain 3 / : / Lipocalin / : / Prokaryotic membrane lipoprotein lipid attachment site profile. / 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 / Alpha-Beta Complex / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 2B / Outer surface protein A / Outer surface protein A
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsDing, W. / Lawson, C.L.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structural identification of a key protective B-cell epitope in Lyme disease antigen OspA.
Authors: Ding, W. / Huang, X. / Yang, X. / Dunn, J.J. / Luft, B.J. / Koide, S. / Lawson, C.L.
History
DepositionAug 7, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionOct 11, 2000ID: 2OSP
Revision 1.0Oct 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 9, 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: HYBRIDOMA ANTIBODY LA2 (LIGHT CHAIN)
B: HYBRIDOMA ANTIBODY LA2 (HEAVY CHAIN)
C: HYBRIDOMA ANTIBODY LA2 (LIGHT CHAIN)
D: HYBRIDOMA ANTIBODY LA2 (HEAVY CHAIN)
E: OUTER SURFACE PROTEIN A
F: OUTER SURFACE PROTEIN A


Theoretical massNumber of molelcules
Total (without water)147,8396
Polymers147,8396
Non-polymers00
Water4,648258
1
A: HYBRIDOMA ANTIBODY LA2 (LIGHT CHAIN)
B: HYBRIDOMA ANTIBODY LA2 (HEAVY CHAIN)
F: OUTER SURFACE PROTEIN A


Theoretical massNumber of molelcules
Total (without water)73,9203
Polymers73,9203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-28 kcal/mol
Surface area31630 Å2
MethodPISA
2
C: HYBRIDOMA ANTIBODY LA2 (LIGHT CHAIN)
D: HYBRIDOMA ANTIBODY LA2 (HEAVY CHAIN)
E: OUTER SURFACE PROTEIN A


Theoretical massNumber of molelcules
Total (without water)73,9203
Polymers73,9203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.079, 129.462, 143.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is an Fab/antigen complex composed of chains A, B, and F, or alternately C, D, and E

-
Components

#1: Antibody HYBRIDOMA ANTIBODY LA2 (LIGHT CHAIN) / LA2 FAB


Mass: 23608.090 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source
Details: LA-2 HYBRIDOMA, GIFT OF M.M. SIMON, MAX PLANCK INSTUTUT, FREIBURG
Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837*PLUS
#2: Antibody HYBRIDOMA ANTIBODY LA2 (HEAVY CHAIN) / LA2 FAB


Mass: 22629.268 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Details: LA-2 HYBRIDOMA / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01867*PLUS
#3: Protein OUTER SURFACE PROTEIN A / OSPA


Mass: 27682.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: B31 / Plasmid: PET9C / Production host: Escherichia coli (E. coli) / References: UniProt: P14013, UniProt: P0CL66*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.15
Details: 100 mM sodium cacodylate, 100 mM sodium acetate, 10 % (w/v) PEG 3350, pH 6.15, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2100 mMsodium cacodylate1reservoir
3100 mMsodium acetate1reservoir
410 %(w/v)PEG33501reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: BRANDEIS / Detector: CCD / Date: May 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.68→20 Å / Num. all: 51741 / Num. obs: 221681 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.9
Reflection shellResolution: 2.68→2.78 Å / Redundancy: 4 % / Rmerge(I) obs: 0.112 / Num. unique all: 5136 / % possible all: 98.4
Reflection
*PLUS
Num. obs: 51741 / Num. measured all: 221681
Reflection shell
*PLUS
% possible obs: 98.4 % / Num. unique obs: 5136 / Num. measured obs: 20967

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GAF, PDB ENTRY 1OSP

1gaf

1osp


Resolution: 2.68→19.83 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1428286.9 / Data cutoff high rms absF: 1428286.9 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 5165 10.1 %RANDOM, 10%
Rwork0.226 ---
all-51197 --
obs-51197 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.6764 Å2 / ksol: 0.318791 e/Å3
Displacement parametersBiso mean: 52.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.16 Å20 Å20 Å2
2---5.25 Å20 Å2
3---8.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.68→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10284 0 0 258 10542
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.94
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.68→2.85 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 822 9.9 %
Rwork0.275 7449 -
obs--94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

+
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