[English] 日本語
Yorodumi
- PDB-2b2x: VLA1 RdeltaH I-domain complexed with a quadruple mutant of the AQ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2b2x
TitleVLA1 RdeltaH I-domain complexed with a quadruple mutant of the AQC2 Fab
Components
  • (Antibody AQC2 Fab) x 2
  • Integrin alpha-1
KeywordsIMMUNE SYSTEM / computational design / antibody-antigen complex
Function / homology
Function and homology information


Integrin cell surface interactions / Smooth Muscle Contraction / cellular extravasation / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / basal part of cell / integrin complex / cell adhesion mediated by integrin / negative regulation of epidermal growth factor receptor signaling pathway / positive regulation of phosphoprotein phosphatase activity ...Integrin cell surface interactions / Smooth Muscle Contraction / cellular extravasation / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / basal part of cell / integrin complex / cell adhesion mediated by integrin / negative regulation of epidermal growth factor receptor signaling pathway / positive regulation of phosphoprotein phosphatase activity / collagen binding / cell chemotaxis / cell-matrix adhesion / neutrophil chemotaxis / neuron projection morphogenesis / acrosomal vesicle / integrin-mediated signaling pathway / cell-cell adhesion / vasodilation / positive regulation of neuron apoptotic process / integrin binding / perikaryon / protein phosphatase binding / positive regulation of MAPK cascade / cell adhesion / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / focal adhesion / cell surface / metal ion binding
Similarity search - Function
: / Integrin alpha Ig-like domain 3 / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site ...: / Integrin alpha Ig-like domain 3 / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsClark, L.A. / Boriack-Sjodin, P.A. / Eldredge, J. / Fitch, C. / Friedman, B. / Hanf, K.J. / Jarpe, M. / Liparoto, S.F. / Li, Y. / Lugovskoy, A.
CitationJournal: Protein Sci. / Year: 2006
Title: Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design
Authors: Clark, L.A. / Boriack-Sjodin, P.A. / Eldredge, J. / Fitch, C. / Friedman, B. / Hanf, K.J. / Jarpe, M. / Liparoto, S.F. / Li, Y. / Lugovskoy, A. / Miller, S. / Rushe, M. / Sherman, W. / ...Authors: Clark, L.A. / Boriack-Sjodin, P.A. / Eldredge, J. / Fitch, C. / Friedman, B. / Hanf, K.J. / Jarpe, M. / Liparoto, S.F. / Li, Y. / Lugovskoy, A. / Miller, S. / Rushe, M. / Sherman, W. / Simon, K. / Van Vlijmen, H.
History
DepositionSep 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE No suitable sequence database references were available for proteins in chains L, H, I and ...SEQUENCE No suitable sequence database references were available for proteins in chains L, H, I and M at the time of processing this entry.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin alpha-1
H: Antibody AQC2 Fab
L: Antibody AQC2 Fab
B: Integrin alpha-1
I: Antibody AQC2 Fab
M: Antibody AQC2 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,6438
Polymers145,5946
Non-polymers492
Water4,071226
1
A: Integrin alpha-1
H: Antibody AQC2 Fab
L: Antibody AQC2 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8224
Polymers72,7973
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-38 kcal/mol
Surface area26100 Å2
MethodPISA
2
B: Integrin alpha-1
I: Antibody AQC2 Fab
M: Antibody AQC2 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8224
Polymers72,7973
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-36 kcal/mol
Surface area25820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.12, 43.68, 153.88
Angle α, β, γ (deg.)90, 104.1, 90
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11H-296-

HOH

Details2 antibody-antigen complexes are in asymmetric unit

-
Components

#1: Protein Integrin alpha-1 / / Laminin and collagen receptor / VLA-1 / CD49a


Mass: 24986.225 Da / Num. of mol.: 2 / Fragment: I domain R delta H / Mutation: G217V, R218Q, Q219R, L222R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Itga1 / Plasmid details: based on pGEX4t-i / Plasmid: pGRTI / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P18614
#2: Antibody Antibody AQC2 Fab


Mass: 24222.035 Da / Num. of mol.: 2 / Fragment: AQC2 Fab Heavy Chain / Mutation: T50V, K64E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: YL037 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10
#3: Antibody Antibody AQC2 Fab


Mass: 23588.947 Da / Num. of mol.: 2 / Fragment: AQC2 Fab Light Chain / Mutation: S28Q, N52Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: YL037 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Peg 20K, Mes, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 66690 / Num. obs: 66690 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.067 / Χ2: 1.499
Reflection shellResolution: 2.2→2.28 Å / % possible obs: 89.5 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.366 / Num. measured obs: 6246 / Χ2: 1.682

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
CNXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MHP

1mhp


Resolution: 2.2→35 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 3380 4.8 %RANDOM
Rwork0.238 ---
all0.241 66690 --
obs0.241 66545 94.3 %-
Displacement parametersBiso mean: 46.159 Å2
Baniso -1Baniso -2Baniso -3
1--3.089 Å20 Å24.979 Å2
2--8.994 Å20 Å2
3----5.905 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9309 0 2 226 9537
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.327
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d26.006
X-RAY DIFFRACTIONc_improper_angle_d0.753
LS refinement shellResolution: 2.2→2.21 Å
RfactorNum. reflection
Rfree0.326 52
Rwork0.3069 -
obs-1164
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

+
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