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- PDB-4cmm: Structure of human CD47 in complex with human Signal Regulatory P... -

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Basic information

Entry
Database: PDB / ID: 4cmm
TitleStructure of human CD47 in complex with human Signal Regulatory Protein (SIRP) alpha v1
Components
  • LEUKOCYTE SURFACE ANTIGEN CD47
  • TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
KeywordsSIGNALING PROTEIN / PAIRED RECEPTOR / IMMUNOLOGICAL / INHIBITORY
Function / homology
Function and homology information


cellular response to interleukin-12 / monocyte extravasation / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of macrophage inflammatory protein 1 alpha production / protein binding involved in heterotypic cell-cell adhesion / negative regulation of chemokine (C-C motif) ligand 5 production / positive regulation of monocyte extravasation / regulation of interleukin-1 beta production / cell-cell adhesion mediator activity / GTPase regulator activity ...cellular response to interleukin-12 / monocyte extravasation / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of macrophage inflammatory protein 1 alpha production / protein binding involved in heterotypic cell-cell adhesion / negative regulation of chemokine (C-C motif) ligand 5 production / positive regulation of monocyte extravasation / regulation of interleukin-1 beta production / cell-cell adhesion mediator activity / GTPase regulator activity / regulation of type II interferon production / positive regulation of cell-cell adhesion / regulation of interleukin-10 production / ATP export / negative regulation of nitric oxide biosynthetic process / protein antigen binding / negative regulation of lipopolysaccharide-mediated signaling pathway / fibrinogen binding / negative regulation of interferon-beta production / regulation of tumor necrosis factor production / negative regulation of JNK cascade / regulation of interleukin-12 production / regulation of nitric oxide biosynthetic process / regulation of interleukin-6 production / Signal regulatory protein family interactions / negative regulation of phagocytosis / protein phosphatase inhibitor activity / thrombospondin receptor activity / negative regulation of interleukin-6 production / tertiary granule membrane / ficolin-1-rich granule membrane / negative regulation of tumor necrosis factor production / cellular response to interleukin-1 / negative regulation of cytokine production involved in inflammatory response / Integrin cell surface interactions / specific granule membrane / positive regulation of phagocytosis / negative regulation of canonical NF-kappaB signal transduction / positive regulation of stress fiber assembly / protein tyrosine kinase binding / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / SH3 domain binding / negative regulation of inflammatory response / cellular response to hydrogen peroxide / positive regulation of T cell activation / positive regulation of inflammatory response / positive regulation of reactive oxygen species metabolic process / cell migration / regulation of gene expression / protein phosphatase binding / angiogenesis / cell adhesion / inflammatory response / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / cell surface / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Leukocyte surface antigen CD47 / CD47-like, transmembrane / CD47 immunoglobulin-like / Leukocyte surface antigen CD47, IgV / CD47 transmembrane region / CD47 immunoglobulin-like domain / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...Leukocyte surface antigen CD47 / CD47-like, transmembrane / CD47 immunoglobulin-like / Leukocyte surface antigen CD47, IgV / CD47 transmembrane region / CD47 immunoglobulin-like domain / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type substrate 1 / Leukocyte surface antigen CD47
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsHatherley, D. / Lea, S.M. / Johnson, S. / Barclay, A.N.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Polymorphisms in the Human Inhibitory Signal-Regulatory Protein Alpha Do not Affect Binding to its Ligand Cd47.
Authors: Hatherley, D. / Lea, S.M. / Johnson, S. / Barclay, A.N.
History
DepositionJan 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 2.0Mar 11, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_database_status / struct_conn
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Dec 20, 2023Group: 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 2.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
B: LEUKOCYTE SURFACE ANTIGEN CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4786
Polymers28,5932
Non-polymers8854
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint11.5 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.390, 32.470, 69.610
Angle α, β, γ (deg.)90.00, 115.06, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1 / SHP SUBSTRATE 1 / SHPS-1 / BRAIN IG-LIKE MOLECULE WITH TYROSINE-BASED ACTIVATION MOTIFS / BIT / ...SHP SUBSTRATE 1 / SHPS-1 / BRAIN IG-LIKE MOLECULE WITH TYROSINE-BASED ACTIVATION MOTIFS / BIT / CD172 ANTIGEN-LIKE FAMILY MEMBER A / INHIBITORY RECEPTOR SHPS-1 / MACROPHAGE FUSION RECEPTOR / MYD-1 ANTIGEN / SIGNAL-REGULATORY PROTEIN ALPHA-1 / SIRP-ALPHA-1 / SIGNAL-REGULATORY PROTEIN ALPHA-2 / SIRP-ALPHA-2 / SIGNAL-REGULATORY PROTEIN ALPHA-3 / SIRP-ALPHA-3 / P84 / SIGNAL REGULATORY PROTEIN SIRP ALPHA V1


Mass: 14074.832 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 31-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEE14 / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Variant (production host): LEC3.2.8.1 / References: UniProt: P78324
#2: Antibody LEUKOCYTE SURFACE ANTIGEN CD47 / ANTIGENIC SURFACE DETERMINANT PROTEIN OA3 / INTEGRIN-ASSOCIATED PROTEIN / IAP / PROTEIN MER6


Mass: 14518.302 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 19-136 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEE14 / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Variant (production host): LEC3.2.8.1 / References: UniProt: Q08722
#3: 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.: 4
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCONTAINS C-TERMINAL HIS-TAG CONTAINS A C-TERMINAL HIS-TAG

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 8.5 / Details: 20% PEG 6000 0.1M TRIS PH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793
DetectorDate: Jun 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.92→34.62 Å / Num. obs: 21067 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 33.87 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.9
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.5 / % possible all: 96

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSXIA2data reduction
XSCALEXIA2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JJS

2jjs


Resolution: 1.92→34.62 Å / Cor.coef. Fo:Fc: 0.9247 / Cor.coef. Fo:Fc free: 0.9146 / SU R Cruickshank DPI: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.156 / SU Rfree Blow DPI: 0.14 / SU Rfree Cruickshank DPI: 0.138
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 1081 5.13 %RANDOM
Rwork0.1926 ---
obs0.1945 21066 98.89 %-
Displacement parametersBiso mean: 39.84 Å2
Baniso -1Baniso -2Baniso -3
1-12.6268 Å20 Å27.7967 Å2
2---14.2183 Å20 Å2
3---1.5916 Å2
Refinement stepCycle: LAST / Resolution: 1.92→34.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 56 174 2074
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111955HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.212659HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d696SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes44HARMONIC2
X-RAY DIFFRACTIONt_gen_planes288HARMONIC5
X-RAY DIFFRACTIONt_it1955HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.17
X-RAY DIFFRACTIONt_other_torsion14.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion277SEMIHARMONIC5
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_contact2276SEMIHARMONIC4
LS refinement shellResolution: 1.92→2.01 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2539 137 5.11 %
Rwork0.2309 2543 -
all0.2322 2680 -
obs--98.89 %

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