[English] 日本語
Yorodumi
- PDB-3pp4: Epitope characterization and crystal structure of GA101 provide i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pp4
TitleEpitope characterization and crystal structure of GA101 provide insights into the molecular basis for the type I / type II distinction of anti- CD20 antibodies
Components
  • B-lymphocyte antigen CD20
  • GA101 Fab heavy chain
  • GA101 Fab light chain
KeywordsIMMUNE SYSTEM / antibody Fab fragment Ig-domain / CD20 / cyclic peptide / antibody antigen
Function / homology
Function and homology information


store-operated calcium entry / positive regulation of calcium ion import across plasma membrane / calcium ion import into cytosol / epidermal growth factor receptor binding / B cell activation / B cell proliferation / plasma membrane raft / immunoglobulin binding / humoral immune response / B cell differentiation ...store-operated calcium entry / positive regulation of calcium ion import across plasma membrane / calcium ion import into cytosol / epidermal growth factor receptor binding / B cell activation / B cell proliferation / plasma membrane raft / immunoglobulin binding / humoral immune response / B cell differentiation / protein tetramerization / B cell receptor signaling pathway / response to bacterium / MHC class II protein complex binding / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane
Similarity search - Function
CD20-like family / Membrane-spanning 4-domains subfamily A / CD20-like family / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
B-lymphocyte antigen CD20
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHopfner, K.-P. / Lammens, A.
CitationJournal: Blood / Year: 2011
Title: Epitope characterization and crystal structure of GA101 provide insights into the molecular basis for type I/II distinction of CD20 antibodies.
Authors: Niederfellner, G. / Lammens, A. / Mundigl, O. / Georges, G.J. / Schaefer, W. / Schwaiger, M. / Franke, A. / Wiechmann, K. / Jenewein, S. / Slootstra, J.W. / Timmerman, P. / Brannstrom, A. / ...Authors: Niederfellner, G. / Lammens, A. / Mundigl, O. / Georges, G.J. / Schaefer, W. / Schwaiger, M. / Franke, A. / Wiechmann, K. / Jenewein, S. / Slootstra, J.W. / Timmerman, P. / Brannstrom, A. / Lindstrom, F. / Mossner, E. / Umana, P. / Hopfner, K.P. / Klein, C.
History
DepositionNov 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
H: GA101 Fab heavy chain
L: GA101 Fab light chain
P: B-lymphocyte antigen CD20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8224
Polymers50,7873
Non-polymers351
Water13,673759
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-42 kcal/mol
Surface area21090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.050, 85.900, 72.870
Angle α, β, γ (deg.)90.00, 116.34, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Antibody GA101 Fab heavy chain


Mass: 23969.881 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Chinese hamster ovary (CHO) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody GA101 Fab light chain


Mass: 23964.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Chinese hamster ovary (CHO) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide B-lymphocyte antigen CD20 / B-lymphocyte surface antigen B1 / Bp35 / Leukocyte surface antigen Leu-16 / Membrane-spanning 4- ...B-lymphocyte surface antigen B1 / Bp35 / Leukocyte surface antigen Leu-16 / Membrane-spanning 4-domains subfamily A member 1


Mass: 2852.051 Da / Num. of mol.: 1 / Fragment: large extracellular loop (UNP residues 163-187) / Source method: obtained synthetically / Details: CD20 / Source: (synth.) Homo sapiens (human) / References: UniProt: P11836
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 759 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16% (w/v) PEG4000, 4% (v/v) isopropanol, 0.1 M sodium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2008
RadiationMonochromator: Silicon (1 1 1) channel-cut / 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. all: 61332 / Num. obs: 60342 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.055 / Rsym value: 0.043 / Net I/σ(I): 17.9
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 5.9 / Rsym value: 0.21 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
EXESdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PP3

3pp3


Resolution: 1.6→42.95 Å / SU ML: 0.17 / σ(F): 1.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 2000 3.31 %RANDOM
Rwork0.1373 ---
obs0.139 60342 98.57 %-
all-61332 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.508 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1319 Å20 Å22.5823 Å2
2---0.3777 Å2-0 Å2
3----7.3775 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3532 0 1 759 4292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043878
X-RAY DIFFRACTIONf_angle_d0.9465354
X-RAY DIFFRACTIONf_dihedral_angle_d15.1921457
X-RAY DIFFRACTIONf_chiral_restr0.06618
X-RAY DIFFRACTIONf_plane_restr0.004687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5994-1.63940.19851380.13544014X-RAY DIFFRACTION95
1.6394-1.68370.20341410.12734129X-RAY DIFFRACTION98
1.6837-1.73320.18641420.11564154X-RAY DIFFRACTION98
1.7332-1.78920.17211420.11124122X-RAY DIFFRACTION98
1.7892-1.85310.1811420.11044168X-RAY DIFFRACTION99
1.8531-1.92730.19871440.11754170X-RAY DIFFRACTION99
1.9273-2.0150.1881420.11974159X-RAY DIFFRACTION99
2.015-2.12130.18141440.12054188X-RAY DIFFRACTION99
2.1213-2.25420.20091440.12424207X-RAY DIFFRACTION99
2.2542-2.42820.19481430.13274163X-RAY DIFFRACTION99
2.4282-2.67250.19031440.13774218X-RAY DIFFRACTION100
2.6725-3.05920.18621450.13974222X-RAY DIFFRACTION100
3.0592-3.85380.16941460.12664249X-RAY DIFFRACTION100
3.8538-42.96550.15851430.14274179X-RAY DIFFRACTION97

+
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://pdbjlc1.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