[English] 日本語
Yorodumi
- PDB-3eoa: Crystal structure the Fab fragment of Efalizumab in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3eoa
TitleCrystal structure the Fab fragment of Efalizumab in complex with LFA-1 I domain, Form I
Components
  • Efalizumab Fab fragment, heavy chain
  • Efalizumab Fab fragment, light chain
  • Integrin alpha-L
KeywordsIMMUNE SYSTEM/CELL ADHESION / Efalizumab / Fab / antibody / LFA-1 / CD11a / I domain / Alternative splicing / Calcium / Glycoprotein / Integrin / Magnesium / Membrane / Polymorphism / Receptor / Transmembrane / IMMUNE SYSTEM-CELL ADHESION COMPLEX
Function / homology
Function and homology information


memory T cell extravasation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX3 Regulates Immune Response and Cell Migration / heterophilic cell-cell adhesion / integrin complex / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / receptor clustering ...memory T cell extravasation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX3 Regulates Immune Response and Cell Migration / heterophilic cell-cell adhesion / integrin complex / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / receptor clustering / phagocytosis / Integrin cell surface interactions / specific granule membrane / cell adhesion molecule binding / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell adhesion / inflammatory response / external side of plasma membrane / Neutrophil degranulation / cell surface / signal transduction / extracellular exosome / metal ion binding / membrane / plasma membrane
Similarity search - Function
Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 ...Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLi, S. / Ding, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Efalizumab binding to the LFA-1 alphaL I domain blocks ICAM-1 binding via steric hindrance.
Authors: Li, S. / Wang, H. / Peng, B. / Zhang, M. / Zhang, D. / Hou, S. / Guo, Y. / Ding, J.
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2009Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Efalizumab Fab fragment, light chain
A: Efalizumab Fab fragment, light chain
H: Efalizumab Fab fragment, heavy chain
B: Efalizumab Fab fragment, heavy chain
I: Integrin alpha-L
J: Integrin alpha-L


Theoretical massNumber of molelcules
Total (without water)135,7336
Polymers135,7336
Non-polymers00
Water6,413356
1
L: Efalizumab Fab fragment, light chain
H: Efalizumab Fab fragment, heavy chain
I: Integrin alpha-L


Theoretical massNumber of molelcules
Total (without water)67,8663
Polymers67,8663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Efalizumab Fab fragment, light chain
B: Efalizumab Fab fragment, heavy chain
J: Integrin alpha-L


Theoretical massNumber of molelcules
Total (without water)67,8663
Polymers67,8663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.719, 81.696, 281.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody Efalizumab Fab fragment, light chain


Mass: 23436.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGG1
#2: Antibody Efalizumab Fab fragment, heavy chain


Mass: 23751.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGG1
#3: Protein Integrin alpha-L / Leukocyte adhesion glycoprotein LFA-1 alpha chain / LFA-1A / Leukocyte function-associated molecule ...Leukocyte adhesion glycoprotein LFA-1 alpha chain / LFA-1A / Leukocyte function-associated molecule 1 alpha chain / CD11 antigen-like family member A


Mass: 20678.686 Da / Num. of mol.: 2 / Fragment: I domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAL, CD11A / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20701
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.1M sodium citric, 0.2M sodium potassium tartrate, 1.6M ammonium sulfate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 24, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 37885 / Num. obs: 37165 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.5 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 21.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3139 / Rsym value: 0.343 / % possible all: 84.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A0Q, 1ZOP

1a0q

1zop


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.873 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26438 1850 5 %RANDOM
Rwork0.22475 ---
obs0.22672 35307 98.05 %-
all-36009 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.434 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--1.61 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9448 0 0 356 9804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229660
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.95413092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46351208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05724.627402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.127151638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8711532
X-RAY DIFFRACTIONr_chiral_restr0.0850.21470
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027210
X-RAY DIFFRACTIONr_nbd_refined0.1960.24143
X-RAY DIFFRACTIONr_nbtor_refined0.3050.26372
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2440
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.212
X-RAY DIFFRACTIONr_mcbond_it0.8551.56040
X-RAY DIFFRACTIONr_mcangle_it1.53929774
X-RAY DIFFRACTIONr_scbond_it1.30233620
X-RAY DIFFRACTIONr_scangle_it2.0164.53318
X-RAY DIFFRACTIONr_rigid_bond_restr1.27539660
X-RAY DIFFRACTIONr_sphericity_free0.783356
X-RAY DIFFRACTIONr_sphericity_bonded0.40639442
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 113 -
Rwork0.319 2149 -
obs--83.38 %

+
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