[English] 日本語
Yorodumi
- PDB-3bkm: Structure of anti-amyloid-beta Fab WO2 (Form A, P212121) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bkm
TitleStructure of anti-amyloid-beta Fab WO2 (Form A, P212121)
Components
  • WO2 IgG2a Fab fragment Heavy Chain
  • WO2 IgG2a Fab fragment Light Chain Kappa
KeywordsIMMUNE SYSTEM / Abeta / amyloid beta peptide / Fab / WO2 / alzheimer's disease / immunotherapies / APP
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / extracellular region / metal ion binding
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
If kappa light chain / Ig heavy chain Mem5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsMiles, L.A. / Wun, K.S. / Crespi, G.A. / Fodero-Tavoletti, M. / Galatis, D. / Bageley, C.J. / Beyreuther, K. / Masters, C.L. / Cappai, R. / McKinstry, W.J. ...Miles, L.A. / Wun, K.S. / Crespi, G.A. / Fodero-Tavoletti, M. / Galatis, D. / Bageley, C.J. / Beyreuther, K. / Masters, C.L. / Cappai, R. / McKinstry, W.J. / Barnham, K.J. / Parker, M.W.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Amyloid-beta-anti-amyloid-beta complex structure reveals an extended conformation in the immunodominant B-cell epitope.
Authors: Miles, L.A. / Wun, K.S. / Crespi, G.A. / Fodero-Tavoletti, M.T. / Galatis, D. / Bagley, C.J. / Beyreuther, K. / Masters, C.L. / Cappai, R. / McKinstry, W.J. / Barnham, K.J. / Parker, M.W.
History
DepositionDec 7, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: WO2 IgG2a Fab fragment Light Chain Kappa
H: WO2 IgG2a Fab fragment Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3625
Polymers52,2512
Non-polymers1113
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-64.7 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.447, 90.496, 123.279
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody WO2 IgG2a Fab fragment Light Chain Kappa


Mass: 27817.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: balb/c / References: UniProt: A2NHM3*PLUS
#2: Antibody WO2 IgG2a Fab fragment Heavy Chain


Mass: 24433.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: balb/c / References: UniProt: P84751*PLUS
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 100mM MES, 10mM ZnSO4, 20% (v/v)PEG 550 monoethylether, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 6, 2004
Details: bent conical Si-mirror (Rh coating); bent cylindrical Ge(111) monochromator
RadiationMonochromator: bent cylindrical Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→19.94 Å / Num. all: 76778 / Num. obs: 76623 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 16.6
Reflection shellResolution: 1.598→1.64 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 16.6 / Num. unique all: 5010 / % possible all: 88.08

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementStarting model: PDB entry 1PLG

1plg


Resolution: 1.6→19.9 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.689 / SU ML: 0.06 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 7623 9.9 %RANDOM
Rwork0.203 ---
all0.22 69155 --
obs0.205 68579 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.181 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3415 0 3 482 3900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223502
X-RAY DIFFRACTIONr_bond_other_d0.0010.022356
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9524771
X-RAY DIFFRACTIONr_angle_other_deg0.8863.0035743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5055440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13623.478138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18415567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1141519
X-RAY DIFFRACTIONr_chiral_restr0.0930.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023869
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02709
X-RAY DIFFRACTIONr_nbd_refined0.2140.2581
X-RAY DIFFRACTIONr_nbd_other0.2030.22495
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21664
X-RAY DIFFRACTIONr_nbtor_other0.0870.21927
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2335
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0710.21
X-RAY DIFFRACTIONr_metal_ion_refined0.3590.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5050.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3120.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.228
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined1.6070.21
X-RAY DIFFRACTIONr_mcbond_it0.8111.52202
X-RAY DIFFRACTIONr_mcbond_other0.2071.5888
X-RAY DIFFRACTIONr_mcangle_it1.57223587
X-RAY DIFFRACTIONr_scbond_it2.45331359
X-RAY DIFFRACTIONr_scangle_it3.7014.51184
LS refinement shellResolution: 1.598→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 513 -
Rwork0.281 4497 -
all-5010 -
obs-5010 88.08 %

+
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