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- PDB-2uv3: Structure of the signal-regulatory protein (SIRP) alpha domain th... -

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Basic information

Entry
Database: PDB / ID: 2uv3
TitleStructure of the signal-regulatory protein (SIRP) alpha domain that binds CD47.
ComponentsTYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
KeywordsRECEPTOR / CD47-BINDING DOMAIN OF SIRP-ALPHA / MEMBRANE / SH3- BINDING / GLYCOPROTEIN / TRANSMEMBRANE / PHOSPHORYLATION / HUMAN SIRP-ALPHA N TERMINAL V DOMAIN / IMMUNOGLOBULIN DOMAIN / SIGNAL-REGULATORY PROTEIN ALPHA
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: 1.8 Å
AuthorsHatherley, D. / Harlos, K. / Dunlop, D.C. / Stuart, D.I. / Barclay, A.N.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Structure of the Macrophage Signal Regulatory Protein Alpha (Sirpalpha) Inhibitory Receptor Reveals a Binding Face Reminiscent of that Used by T Cell Receptors.
Authors: Hatherley, D. / Harlos, K. / Dunlop, D.C. / Stuart, D.I. / Barclay, A.N.
History
DepositionMar 8, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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


Theoretical massNumber of molelcules
Total (without water)28,80610
Polymers27,8392
Non-polymers9678
Water5,368298
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-15.5 kcal/mol
Surface area17200 Å2
MethodPQS
Unit cell
Length a, b, c (Å)76.831, 56.266, 82.245
Angle α, β, γ (deg.)90.00, 114.90, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116B3 - 120
2116A3 - 120

NCS oper: (Code: given
Matrix: (0.6387, -0.01612, 0.7693), (-0.004744, -0.9998, -0.01701), (0.7695, 0.007215, -0.6386)
Vector: -9.811, 88.21, 22.18)

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Components

#1: Protein TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1 / SIGNAL-REGULATORY PROTEIN ALPHA N-TERMINAL DOMAIN / SHP SUBSTRATE 1 / SHPS-1 / INHIBITORY RECEPTOR ...SIGNAL-REGULATORY PROTEIN ALPHA N-TERMINAL DOMAIN / SHP SUBSTRATE 1 / SHPS-1 / INHIBITORY RECEPTOR SHPS-1 / SIGNAL-REGULATORY PROTEIN ALPHA-1 / SIRP-ALPHA-1 / SIRP-ALPHA-2 / SIRP-ALPHA-3 / MYD-1 ANTIGEN / BRAIN IG-LIKE MOLECULE WITH TYROSINE-BASED ACTIVATION MOTIFS / BIT / MACROPHAGE FUSION RECEPTOR / P84 / CD172A ANTIGEN


Mass: 13919.563 Da / Num. of mol.: 2 / Fragment: CD47 BINDING DOMAIN, RESIDUES 31-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell (production host): OVARY / Production host: CRICETULUS GRISEUS (Chinese hamster) / Variant (production host): LEC3.2.8.1 / References: UniProt: P78324
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDIFFERENCES AT C-TERMINUS DUE TO EXPRESSION VECTOR CONSTRUCT (HIS TAGGED)

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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: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 6 / Details: 2.4 M AMMONIUM SULPHATE, 0.1 M MES, PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8856, 0.9783, 0.9079, 0.9792
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.88561
20.97831
30.90791
40.97921
ReflectionResolution: 1.8→50 Å / Num. obs: 441122 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.8 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE DETERMINED BY MAD IN SPACE GROUP P21212

Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.902 / SU B: 4.713 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1497 5.1 %RANDOM
Rwork0.204 ---
obs0.207 28037 99 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.85 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å20 Å20.82 Å2
2---1.77 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 0 54 298 2206
Refine LS restraints NCS

Ens-ID: 1 / Number: 1458 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Bloose positional0.550
2Aloose thermal1.64100
LS refinement shellResolution: 1.8→1.84 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 90
Rwork0.215 1982
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)
10.74780.5656-0.28382.1611-0.77482.6348-0.05670.0218-0.0532-0.1899-0.0498-0.12050.21080.11770.1064-0.11210.02580.008-0.10850.0072-0.135120.16342.1969.064
21.1475-0.0299-0.21911.491-0.5981.29830.0982-0.05670.05690.0375-0.02570.0077-0.16370.0252-0.0725-0.1701-0.016-0.0186-0.1187-0.0077-0.13139.20344.81632.966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 121
2X-RAY DIFFRACTION2B2 - 123

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