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- PDB-2wng: complete extracellular structure of human signal regulatory prote... -

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Basic information

Entry
Database: PDB / ID: 2wng
Titlecomplete extracellular structure of human signal regulatory protein (SIRP) alpha
ComponentsTYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
KeywordsCELL ADHESION / SIGNAL REGULATORY PROTEIN ALPHA / IMMUNOGLOBULIN SUPERFAMILY / PHOSPHOPROTEIN / DISULFIDE BOND / PAIRED RECEPTOR / ALTERNATIVE SPLICING / IMMUNOGLOBULIN DOMAIN / SIRP / CD47 / SIRPA / MEMBRANE / SH3-BINDING / POLYMORPHISM / GLYCOPROTEIN / TRANSMEMBRANE
Function / homology
Function and homology information


negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / protein binding involved in heterotypic cell-cell adhesion / regulation of interleukin-1 beta production / regulation of type II interferon production / cell-cell adhesion mediator activity / GTPase regulator activity ...negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / protein binding involved in heterotypic cell-cell adhesion / regulation of interleukin-1 beta production / regulation of type II interferon production / cell-cell adhesion mediator activity / GTPase regulator activity / protein antigen binding / negative regulation of nitric oxide biosynthetic process / negative regulation of interferon-beta production / negative regulation of JNK cascade / regulation of tumor necrosis factor production / regulation of nitric oxide biosynthetic process / negative regulation of phagocytosis / regulation of interleukin-6 production / Signal regulatory protein family interactions / tertiary granule membrane / negative regulation of interleukin-6 production / ficolin-1-rich granule membrane / negative regulation of tumor necrosis factor production / negative regulation of cytokine production involved in inflammatory response / cellular response to interleukin-1 / positive regulation of phagocytosis / protein tyrosine kinase binding / negative regulation of protein phosphorylation / Cell surface interactions at the vascular wall / negative regulation of ERK1 and ERK2 cascade / cellular response to hydrogen peroxide / negative regulation of inflammatory response / SH3 domain binding / cellular response to type II interferon / positive regulation of T cell activation / cell migration / regulation of gene expression / protein phosphatase binding / cellular response to lipopolysaccharide / cell adhesion / Neutrophil degranulation / cell surface / extracellular exosome / membrane / plasma membrane
Similarity search - Function
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 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type substrate 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsHatherley, D. / Graham, S.C. / Harlos, K. / Stuart, D.I. / Barclay, A.N.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure of Signal-Regulatory Protein Alpha: A Link to Antigen Receptor Evolution.
Authors: Hatherley, D. / Graham, S.C. / Harlos, K. / Stuart, D.I. / Barclay, A.N.
History
DepositionJul 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Dec 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4262
Polymers36,2041
Non-polymers2211
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.410, 84.370, 98.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 36204.328 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN, RESIDUES 31-319
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: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFINAL 8 RESIDUES (TRHHHHHH) ARE DERIVED FROM THE EXPRESSION VECTOR.

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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: 2.85 Å3/Da / Density % sol: 56.9 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: SITTING DROPS CONTAINING 100 NL SIRP (18.6 MG/ML) PLUS 100 NL PRECIPITANT (1.0 M TRI-SODIUM CITRATE, 0.1 M SODIUM CACODYLATE, PH 6.5) WERE EQUILIBRATED AT 20.5C AGAINST 95 UL RESERVOIRS OF ...Details: SITTING DROPS CONTAINING 100 NL SIRP (18.6 MG/ML) PLUS 100 NL PRECIPITANT (1.0 M TRI-SODIUM CITRATE, 0.1 M SODIUM CACODYLATE, PH 6.5) WERE EQUILIBRATED AT 20.5C AGAINST 95 UL RESERVOIRS OF PRECIPITANT. CRYSTALS WERE CRYO-PROTECTED BY A QUICK SWEEP THROUGH PERFLUOROPOLYETHER PFO-X125/03 (LANCASTER SYNTHESIS).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 27, 2007 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.49→38.1 Å / Num. obs: 14246 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 62.638 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.2
Reflection shellResolution: 2.49→2.55 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER-TNT2.5.1refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2UV3, 2AJR AND 1ED3

2uv3

2ajr

1ed3


Resolution: 2.49→27.05 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: REMARK 3
RfactorNum. reflection% reflectionSelection details
Rfree0.2714 692 4.9 %RANDOM
Rwork0.2188 ---
obs0.2212 14207 97.91 %-
Displacement parametersBiso mean: 62.71 Å2
Baniso -1Baniso -2Baniso -3
1--11.72294167 Å20 Å20 Å2
2---0.94041704 Å20 Å2
3---12.66335871 Å2
Refinement stepCycle: LAST / Resolution: 2.49→27.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 14 49 2413
LS refinement shellResolution: 2.49→2.64 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3282 106 4.73 %
Rwork0.2814 2133 -
all0.2836 2239 -
obs--97.91 %

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