[English] 日本語
Yorodumi
- PDB-5dfv: CRYSTAL STRUCTURE OF HUMAN CD81 LARGE EXTRACELLULAR LOOP IN COMPL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dfv
TitleCRYSTAL STRUCTURE OF HUMAN CD81 LARGE EXTRACELLULAR LOOP IN COMPLEX WITH MURINE FAB FRAGMENT K04
Components
  • CD81 antigen
  • FAB HEAVY CHAIN
  • FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / HELICAL BUNDLE / CELL ADHESION / ANTIBODY-ANTIGEN COMPLEX
Function / homology
Function and homology information


positive regulation of adaptive immune memory response / positive regulation of protein catabolic process in the vacuole / CD4-positive, alpha-beta T cell costimulation / osteoclast fusion / positive regulation of B cell receptor signaling pathway / myoblast fusion involved in skeletal muscle regeneration / positive regulation of inflammatory response to antigenic stimulus / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of macrophage migration / macrophage fusion ...positive regulation of adaptive immune memory response / positive regulation of protein catabolic process in the vacuole / CD4-positive, alpha-beta T cell costimulation / osteoclast fusion / positive regulation of B cell receptor signaling pathway / myoblast fusion involved in skeletal muscle regeneration / positive regulation of inflammatory response to antigenic stimulus / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of macrophage migration / macrophage fusion / transferrin receptor binding / immunological synapse formation / positive regulation of T-helper 2 cell cytokine production / protein localization to lysosome / tetraspanin-enriched microdomain / positive regulation of protein exit from endoplasmic reticulum / MHC class II protein binding / humoral immune response mediated by circulating immunoglobulin / positive regulation of CD4-positive, alpha-beta T cell proliferation / cholesterol binding / positive regulation of T cell receptor signaling pathway / cellular response to low-density lipoprotein particle stimulus / immunological synapse / positive regulation of B cell proliferation / positive regulation of receptor clustering / basal plasma membrane / Regulation of Complement cascade / protein localization to plasma membrane / regulation of protein stability / receptor internalization / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / MHC class II protein complex binding / virus receptor activity / basolateral plasma membrane / vesicle / positive regulation of MAPK cascade / focal adhesion / positive regulation of transcription by RNA polymerase II / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Cd81 Antigen, Extracellular Domain; Chain: A / Tetraspanin / Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / Immunoglobulins / Immunoglobulin-like ...Cd81 Antigen, Extracellular Domain; Chain: A / Tetraspanin / Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHarris, S.F. / Wong, A. / Kuglstatter, A.
CitationJournal: Mabs / Year: 2016
Title: VH-VL orientation prediction for antibody humanization candidate selection: A case study.
Authors: Bujotzek, A. / Lipsmeier, F. / Harris, S.F. / Benz, J. / Kuglstatter, A. / Georges, G.
History
DepositionAug 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CD81 antigen
B: CD81 antigen
C: FAB HEAVY CHAIN
D: FAB LIGHT CHAIN
E: FAB HEAVY CHAIN
F: FAB LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)117,1796
Polymers117,1796
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12660 Å2
ΔGint-87 kcal/mol
Surface area44290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.631, 94.483, 94.114
Angle α, β, γ (deg.)90.00, 104.14, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CD81 antigen / 26 kDa cell surface protein TAPA-1 / Target of the antiproliferative antibody 1 / Tetraspanin-28 / Tspan-28


Mass: 10947.140 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD81, TAPA1, TSPAN28 / Production host: Escherichia coli (E. coli) / References: UniProt: P60033
#2: Antibody FAB HEAVY CHAIN


Mass: 23454.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: MURINE HYBRIDOMA
#3: Antibody FAB LIGHT CHAIN


Mass: 24187.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: MURINE HYBRIDOMA
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M NaOAc, 20% PEG 10000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 30682 / % possible obs: 94 % / Redundancy: 3.4 % / Rsym value: 0.125 / Net I/σ(I): 7.1
Reflection shellResolution: 2.8→2.93 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.4 / % possible all: 63.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.25 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.83 / SU B: 17.241 / SU ML: 0.332 / Cross valid method: THROUGHOUT / ESU R Free: 0.442 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29066 1583 5.2 %RANDOM
Rwork0.23947 ---
obs0.24213 29086 93.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.375 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.64 Å2
2---0.07 Å20 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 2.8→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7936 0 0 5 7941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228109
X-RAY DIFFRACTIONr_bond_other_d0.0010.025428
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.9511014
X-RAY DIFFRACTIONr_angle_other_deg0.7853.00313300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08451026
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81824.798321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.532151347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0231526
X-RAY DIFFRACTIONr_chiral_restr0.0610.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028961
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021555
X-RAY DIFFRACTIONr_nbd_refined0.2020.21747
X-RAY DIFFRACTIONr_nbd_other0.1810.25512
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23865
X-RAY DIFFRACTIONr_nbtor_other0.0830.24509
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3651.56596
X-RAY DIFFRACTIONr_mcbond_other0.031.52084
X-RAY DIFFRACTIONr_mcangle_it0.40428336
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.41333530
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.6774.52678
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 66 -
Rwork0.364 1250 -
obs--54.83 %

+
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://pdbjlvh1.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