[English] 日本語
Yorodumi
- PDB-5m4r: Structural tuning of CD81LEL (space group C2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m4r
TitleStructural tuning of CD81LEL (space group C2)
ComponentsCD81 antigen
KeywordsCELL ADHESION / human cellular receptor for Hepatitis C virus
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsCunha, E.S. / Sfriso, P. / Rojas, A.L. / Roversi, P. / Hospital, A. / Orozco, M. / Abrescia, N.G.
Funding support Spain, 3items
OrganizationGrant numberCountry
MINECOBIO2012-32868 Spain
MINECOBFU2012-33947 Spain
MINECOBFU2015-64541-R Spain
Citation
Journal: Structure / Year: 2017
Title: Mechanism of Structural Tuning of the Hepatitis C Virus Human Cellular Receptor CD81 Large Extracellular Loop.
Authors: Cunha, E.S. / Sfriso, P. / Rojas, A.L. / Roversi, P. / Hospital, A. / Orozco, M. / Abrescia, N.G.
#1: Journal: EMBO J. / Year: 2001
Title: CD81 extracellular domain 3D structure: insight into the tetraspanin superfamily structural motifs.
Authors: Kitadokoro, K. / Bordo, D. / Galli, G. / Petracca, R. / Falugi, F. / Abrignani, S. / Grandi, G. / Bolognesi, M.
#2: Journal: Biol. Chem. / Year: 2002
Title: Subunit association and conformational flexibility in the head subdomain of human CD81 large extracellular loop.
Authors: Kitadokoro, K. / Ponassi, M. / Galli, G. / Petracca, R. / Falugi, F. / Grandi, G. / Bolognesi, M.
History
DepositionOct 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Dec 13, 2017Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CD81 antigen
B: CD81 antigen
C: CD81 antigen
D: CD81 antigen
E: CD81 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,38611
Polymers55,9125
Non-polymers4746
Water00
1
A: CD81 antigen
D: CD81 antigen


Theoretical massNumber of molelcules
Total (without water)22,3652
Polymers22,3652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-16 kcal/mol
Surface area9090 Å2
MethodPISA
2
B: CD81 antigen
E: CD81 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6816
Polymers22,3652
Non-polymers3164
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-33 kcal/mol
Surface area9120 Å2
MethodPISA
3
C: CD81 antigen
hetero molecules

C: CD81 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6816
Polymers22,3652
Non-polymers3164
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2250 Å2
ΔGint-51 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.120, 104.970, 65.010
Angle α, β, γ (deg.)90.00, 99.44, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 115:136 or resseq 143:160 or resseq 188:200 ) and (not element H)
211chain B and (resseq 115:136 or resseq 143:160 or resseq 188:200 ) and (not element H)
311chain D and (resseq 115:136 or resseq 143:160 or resseq 188:200 ) and (not element H)
411chain C and (resseq 115:136 or resseq 143:160 or resseq 188:200 ) and (not element H)
511chain E and (resseq 115:136 or resseq 143:160 or resseq 188:200 ) and (not element H)

NCS ensembles :
ID
1
2
3
4
5

-
Components

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


Mass: 11182.417 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: in chain E the last residue has been modelled as ALA
Source: (gene. exp.) Homo sapiens (human) / Gene: CD81, TAPA1, TSPAN28 / Plasmid: pHLSec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P60033
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.1 %
Description: small (about 40x60x15 microns) brick-like morphology weak diffractor but reasonable to 3.1 Ang
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 4
Details: Protein: ~10mg/ml Buffer: 0.1 M NaCitrate pH 4.0, 0.8 M (NH4)2 SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.1→53.1 Å / Num. obs: 15510 / % possible obs: 98.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.1
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2 / CC1/2: 0.817 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G8Q

1g8q


Resolution: 3.1→53.093 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 31.61
RfactorNum. reflection% reflection
Rfree0.2459 762 4.98 %
Rwork0.2256 --
obs0.2267 15306 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→53.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 27 0 3322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073358
X-RAY DIFFRACTIONf_angle_d0.9584514
X-RAY DIFFRACTIONf_dihedral_angle_d12.3741207
X-RAY DIFFRACTIONf_chiral_restr0.031541
X-RAY DIFFRACTIONf_plane_restr0.003585
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A413X-RAY DIFFRACTIONPOSITIONAL
12B413X-RAY DIFFRACTIONPOSITIONAL0.025
13D413X-RAY DIFFRACTIONPOSITIONAL0.063
14C413X-RAY DIFFRACTIONPOSITIONAL0.06
15E413X-RAY DIFFRACTIONPOSITIONAL0.026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.33930.28541370.26312746X-RAY DIFFRACTION93
3.3393-3.67530.28391430.26872949X-RAY DIFFRACTION99
3.6753-4.2070.25531530.232939X-RAY DIFFRACTION99
4.207-5.29960.24021560.21042961X-RAY DIFFRACTION99
5.2996-53.10060.2281730.21092949X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.5144-0.6294-0.3549.39240.12737.63390.1640.26790.3772-0.4783-0.16480.3351-0.3418-0.3612-0.04660.9196-0.04350.02780.7545-0.02140.539717.2093-7.63223.3515
21.92710.0855-0.25774.62242.70794.2390.08030.11060.5230.52650.7361-1.1052-1.73711.6101-0.67591.1203-0.25030.15850.9487-0.11810.960929.0082-7.509316.6151
37.24162.16711.12676.8339-0.55157.023-0.28390.2201-0.6235-0.62160.26930.0162-0.14270.4454-0.01450.7585-0.06830.04610.5172-0.03810.645234.50298.1534-10.7304
42.74161.3655-0.31745.59981.964.49360.371-0.5070.25940.9585-0.42880.07620.8212-0.46480.09650.7262-0.13810.04190.60470.0120.609833.61-0.5041-0.0717
58.7134-0.2133-0.35921.45251.1586.79230.293-0.0595-0.4597-0.1860.1088-0.5498-0.35370.1915-0.42850.5142-0.0379-0.01290.39260.0230.48347.6481-16.6356-1.0368
64.32293.40551.97452.88020.3224.7838-0.20430.11170.63330.08530.16181.1865-2.0014-0.7025-0.14880.93630.1301-0.04340.61180.05820.640916.8076-6.33730.9551
77.47910.30831.25418.21441.32819.84750.4037-0.178-0.46851.0932-0.37120.67340.962-1.40020.03880.8201-0.10660.06460.8360.00480.63114.5711-13.45337.7119
81.63621.0141.08865.12192.14582.63860.62770.0238-0.11920.1025-0.1939-0.84220.23030.4902-0.30961.1816-0.00360.08170.70250.07330.740422.265-14.328949.1799
96.27921.66460.45756.51840.63616.87550.33090.37430.4107-1.3962-0.3306-0.0475-0.6245-0.4990.07190.98520.04320.06920.61830.00680.672333.516923.0963-10.3706
101.48391.063-1.24245.25560.57914.3310.3788-0.9537-0.15251.1921-0.07210.9030.56930.04950.42840.9968-0.07820.16380.6244-0.0690.782234.629632.655-0.6687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 115:157 or resid 189:200)
2X-RAY DIFFRACTION2chain A and (resid 158:188)
3X-RAY DIFFRACTION3chain B and (resid 114:157 or resid 189:200)
4X-RAY DIFFRACTION4chain B and (resid 158:188)
5X-RAY DIFFRACTION5chain C and (resid 114:157 or resid 189:200)
6X-RAY DIFFRACTION6chain C and (resid 158:188)
7X-RAY DIFFRACTION7chain D and (resid 114:157 or resid 189:201)
8X-RAY DIFFRACTION8chain D and (resid 158:188)
9X-RAY DIFFRACTION9chain E and (resid 114:157 or resid 189:203)
10X-RAY DIFFRACTION10chain E and (resid 158:188)

+
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