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- PDB-9sia: Crystal structure of human Signal Regulatory Protein 2 (SIRP) alp... -

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Basic information

Entry
Database: PDB / ID: 9sia
TitleCrystal structure of human Signal Regulatory Protein 2 (SIRP) alpha V2 in complex with L-Tryptophane
Componentshuman SIRP alpha V2
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN SUPERFAMILY / SIRP / SIRPA / DON'T EAT ME SIGNAL / IMMUNE CHECKPOINT / TRYPTOPHANE / COMPLEX
Function / homologyTRYPTOPHAN
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsBarelier, S. / Betzi, S. / Garcin, E.D. / Miller, T.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Biorxiv / Year: 2025
Title: Engineering SIRP alpha conformational plasticity to reveal a cryptic pocket suitable for structure-based drug design.
Authors: Storder, M. / Barelier, S. / Cordier, F. / Yacoub, T. / Ilari, L. / Barral, K. / Mahmoodi, S. / Saez-Ayala, M. / Combes, S. / Betzi, S. / Derviaux, C. / Ulliana, A. / Torres, F. / Rubin, J. ...Authors: Storder, M. / Barelier, S. / Cordier, F. / Yacoub, T. / Ilari, L. / Barral, K. / Mahmoodi, S. / Saez-Ayala, M. / Combes, S. / Betzi, S. / Derviaux, C. / Ulliana, A. / Torres, F. / Rubin, J. / Roche, P. / Morelli, X. / Garcin, E.D. / Miller, T.W.
History
DepositionAug 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: human SIRP alpha V2
B: human SIRP alpha V2
C: human SIRP alpha V2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2248
Polymers38,7583
Non-polymers4665
Water2,558142
1
A: human SIRP alpha V2


Theoretical massNumber of molelcules
Total (without water)12,9191
Polymers12,9191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: human SIRP alpha V2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0503
Polymers12,9191
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: human SIRP alpha V2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2554
Polymers12,9191
Non-polymers3353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.355, 57.355, 198.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein human SIRP alpha V2


Mass: 12919.462 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.01M Zinc sulfate heptahydrate 0.1M MES monohydrate pH 6.5 25% v/v PEG monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.83→43.32 Å / Num. obs: 29981 / % possible obs: 99 % / Redundancy: 7.3 % / CC1/2: 0.998 / Net I/σ(I): 14
Reflection shellResolution: 1.83→1.89 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2905 / CC1/2: 0.596

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→43.32 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2565 1453 4.86 %
Rwork0.217 --
obs0.2189 29893 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→43.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 19 142 2756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092698
X-RAY DIFFRACTIONf_angle_d1.0153666
X-RAY DIFFRACTIONf_dihedral_angle_d6.326373
X-RAY DIFFRACTIONf_chiral_restr0.067412
X-RAY DIFFRACTIONf_plane_restr0.009478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.90.35071480.30422793X-RAY DIFFRACTION100
1.9-1.970.35471390.28272825X-RAY DIFFRACTION100
1.97-2.060.30071560.25142803X-RAY DIFFRACTION100
2.06-2.170.30571430.23262786X-RAY DIFFRACTION99
2.17-2.310.27671300.23322835X-RAY DIFFRACTION99
2.31-2.480.26461570.23362798X-RAY DIFFRACTION99
2.48-2.730.29681450.24062820X-RAY DIFFRACTION98
2.73-3.130.29081310.23422845X-RAY DIFFRACTION98
3.13-3.940.21431360.19682895X-RAY DIFFRACTION98
3.94-43.320.20111680.17063040X-RAY DIFFRACTION97

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