[English] 日本語
Yorodumi
- PDB-5fmv: Crystal structure of human CD45 extracellular region, domains d1-d4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fmv
TitleCrystal structure of human CD45 extracellular region, domains d1-d4
ComponentsRECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
KeywordsHYDROLASE / RECEPTOR PROTEIN TYROSINE PHOSPHATASE / CD45 / PTPRC
Function / homology
Function and homology information


plasma membrane raft distribution / positive regulation of antigen receptor-mediated signaling pathway / positive regulation of hematopoietic stem cell migration / negative regulation of cytokine-mediated signaling pathway / negative regulation of interleukin-4-mediated signaling pathway / alpha-beta T cell proliferation / negative regulation of cell adhesion involved in substrate-bound cell migration / positive regulation of Fc receptor mediated stimulatory signaling pathway / regulation of interleukin-8 production / regulation of T cell receptor signaling pathway ...plasma membrane raft distribution / positive regulation of antigen receptor-mediated signaling pathway / positive regulation of hematopoietic stem cell migration / negative regulation of cytokine-mediated signaling pathway / negative regulation of interleukin-4-mediated signaling pathway / alpha-beta T cell proliferation / negative regulation of cell adhesion involved in substrate-bound cell migration / positive regulation of Fc receptor mediated stimulatory signaling pathway / regulation of interleukin-8 production / regulation of T cell receptor signaling pathway / membrane microdomain / negative regulation of T cell mediated cytotoxicity / negative regulation of microglial cell activation / Other semaphorin interactions / positive regulation of humoral immune response mediated by circulating immunoglobulin / cell cycle phase transition / DN2 thymocyte differentiation / transmembrane receptor protein tyrosine phosphatase activity / natural killer cell differentiation / stem cell development / positive regulation of alpha-beta T cell proliferation / bleb / positive regulation of isotype switching to IgG isotypes / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / negative thymic T cell selection / negative regulation of receptor signaling pathway via JAK-STAT / regulation of phagocytosis / positive thymic T cell selection / response to aldosterone / heparan sulfate proteoglycan binding / protein tyrosine kinase inhibitor activity / dephosphorylation / positive regulation of extrinsic apoptotic signaling pathway / bone marrow development / heterotypic cell-cell adhesion / ankyrin binding / positive regulation of immunoglobulin production / negative regulation of interleukin-2 production / leukocyte cell-cell adhesion / spectrin binding / positive regulation of stem cell proliferation / Phosphorylation of CD3 and TCR zeta chains / positive regulation of protein kinase activity / B cell proliferation / T cell differentiation / hematopoietic progenitor cell differentiation / protein dephosphorylation / negative regulation of protein kinase activity / extrinsic apoptotic signaling pathway / positive regulation of phagocytosis / positive regulation of B cell proliferation / release of sequestered calcium ion into cytosol / positive regulation of T cell proliferation / protein-tyrosine-phosphatase / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / B cell differentiation / protein tyrosine phosphatase activity / T cell activation / secretory granule membrane / response to gamma radiation / B cell receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / positive regulation of T cell mediated cytotoxicity / cytoplasmic side of plasma membrane / positive regulation of tumor necrosis factor production / MAPK cascade / T cell receptor signaling pathway / heparin binding / regulation of gene expression / defense response to virus / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / regulation of cell cycle / positive regulation of MAPK cascade / membrane raft / signaling receptor binding / external side of plasma membrane / focal adhesion / synapse / Neutrophil degranulation / protein kinase binding / cell surface / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase C / Protein tyrosine phosphatase, receptor type, N-terminal / Protein tyrosine phosphatase N terminal / Leukocyte receptor CD45 / : / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic ...Receptor-type tyrosine-protein phosphatase C / Protein tyrosine phosphatase, receptor type, N-terminal / Protein tyrosine phosphatase N terminal / Leukocyte receptor CD45 / : / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase C
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChang, V.T. / Fernandes, R.A. / Ganzinger, K.A. / Lee, S.F. / Siebold, C. / McColl, J. / Jonsson, P. / Palayret, M. / Harlos, K. / Coles, C.H. ...Chang, V.T. / Fernandes, R.A. / Ganzinger, K.A. / Lee, S.F. / Siebold, C. / McColl, J. / Jonsson, P. / Palayret, M. / Harlos, K. / Coles, C.H. / Jones, E.Y. / Lui, Y. / Huang, E. / Gilbert, R.J.C. / Klenerman, D. / Aricescu, A.R. / Davis, S.J.
CitationJournal: Nat.Immunol. / Year: 2016
Title: Initiation of T Cell Signaling by Cd45 Segregation at 'Close Contacts'.
Authors: Chang, V.T. / Fernandes, R.A. / Ganzinger, K.A. / Lee, S.F. / Siebold, C. / Mccoll, J. / Jonsson, P. / Palayret, M. / Harlos, K. / Coles, C.H. / Jones, E.Y. / Lui, Y. / Huang, E. / Gilbert, ...Authors: Chang, V.T. / Fernandes, R.A. / Ganzinger, K.A. / Lee, S.F. / Siebold, C. / Mccoll, J. / Jonsson, P. / Palayret, M. / Harlos, K. / Coles, C.H. / Jones, E.Y. / Lui, Y. / Huang, E. / Gilbert, R.J. / Klenerman, D. / Aricescu, A.R. / Davis, S.J.
History
DepositionNov 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
B: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,21518
Polymers83,3012
Non-polymers2,91416
Water00
1
A: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0459
Polymers41,6511
Non-polymers1,3948
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1709
Polymers41,6511
Non-polymers1,5198
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.550, 59.410, 100.420
Angle α, β, γ (deg.)90.00, 111.66, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C / LEUKOCYTE COMMON ANTIGEN / L-CA / T200 / CD45 EXTRACELLULAR REGION D1-D4


Mass: 41650.668 Da / Num. of mol.: 2 / Fragment: DOMAINS D1-D4, RESIDUES 223-571
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T-CELLS / Plasmid: PEE14 / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P08575, protein-tyrosine-phosphatase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY
Sequence detailsETG N-TERMINAL RESIDUES DERIVED FROM THE EXPRESSION VECTOR. GTKHHHHHH C-TERMINAL RESIDUES DERIVED ...ETG N-TERMINAL RESIDUES DERIVED FROM THE EXPRESSION VECTOR. GTKHHHHHH C-TERMINAL RESIDUES DERIVED FROM THE EXPRESSION VECTOR.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.48 % / Description: NONE
Crystal growpH: 8 / Details: 14% W/V PEG8K, 0.2M (NH4)2SO4, PH=8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 22973 / % possible obs: 98.6 % / Observed criterion σ(I): 1.5 / Redundancy: 3.5 % / Biso Wilson estimate: 75.35 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.9
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.5 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN CD45 EXTRACELLULAR REGION DOMAINS D1- D3

Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.8786 / Cor.coef. Fo:Fc free: 0.8173 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.358
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1161 5.14 %RANDOM
Rwork0.2259 ---
obs0.2271 22584 96.79 %-
Displacement parametersBiso mean: 107.38 Å2
Baniso -1Baniso -2Baniso -3
1-12.336 Å20 Å28.2287 Å2
2--27.8747 Å20 Å2
3----40.2107 Å2
Refine analyzeLuzzati coordinate error obs: 0.601 Å
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5632 0 179 0 5811
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085970HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.158128HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2779SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes174HARMONIC2
X-RAY DIFFRACTIONt_gen_planes849HARMONIC5
X-RAY DIFFRACTIONt_it5970HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion3.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion827SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5964SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.04 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2945 128 4.72 %
Rwork0.2601 2585 -
all0.2617 2713 -
obs--96.79 %
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)
10.1936-0.84921.75123.59391.0293.6147-0.0416-0.05950.08170.0107-0.0023-0.0893-0.0562-0.09040.04390.07370.3532-0.22920.0012-0.1368-0.0479-34.580461.019-2.8435
22.3716-0.69571.37250-0.42532.8581-0.0358-0.11150.03160.0938-0.00840.13690.0675-0.02870.0442-0.05810.4308-0.3810.16530.0228-0.1017-19.5837.91679.0631
32.7063-2.30833.23611.2546-0.28353.63590.11320.5234-0.0622-0.6726-0.13470.3877-0.1732-0.66230.0214-0.06350.1291-0.36240.13330.05470.01131.2606-0.087418.2731
43.8481-1.08170.15654.93250.14631.91050.0337-0.0405-0.1598-0.32660.07520.11790.2085-0.1203-0.1089-0.0541-0.0930.065-0.2037-0.0137-0.048427.225-23.456444.4434
56.1751-3.769-2.99445.0685-0.5136-0.87160.0026-0.0804-0.1362-0.1147-0.0507-0.40930.03170.35370.04810.0650.40660.08460.0777-0.20770.014156.6612-46.440121.0579
64.8032-3.3480.368412.0005-0.45252.7221-0.02230.25710.0826-0.10210.0169-0.1220.02040.14730.0054-0.12810.08810.1234-0.09870.0161-0.276339.2837-23.452227.0401
73.13-3.2177-0.55669.71722.29151.84960.26050.19470.1279-0.2602-0.0288-0.02780.04210.0423-0.2317-0.08090.09040.0104-0.08930.188-0.057316.282213.243826.587
88.7467-2.3735-1.02825.7534-0.67582.4864-0.10250.01310.06790.1192-0.00520.25070.07970.03760.1077-0.1809-0.06890.0651-0.3501-0.0230.2396-16.08836.605444.7014

+
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