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- PDB-9t7f: Crystal structure of human Signal Regulatory Protein 2 (SIRP) alp... -

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Basic information

Entry
Database: PDB / ID: 9t7f
TitleCrystal structure of human Signal Regulatory Protein 2 (SIRP) alpha V2 in complex with 5-Hydroxy-L-Tryptophan
Componentshuman SIRP alpha V2
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN SUPERFAMILY / SIRP / SIRPA / DON'T EAT ME SIGNAL / IMMUNE CHECKPOINT / 5-HYDROX-TRYPTOPHAN / COMPLEX
Function / homology5-hydroxy-L-tryptophan
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBarelier, S. / Barral, K. / 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
DepositionNov 10, 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)39,37110
Polymers38,7583
Non-polymers6137
Water3,711206
1
A: human SIRP alpha V2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9852
Polymers12,9191
Non-polymers651
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)13,3365
Polymers12,9191
Non-polymers4164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.457, 57.457, 198.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-361-

HOH

21B-372-

HOH

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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.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-4PQ / 5-hydroxy-L-tryptophan / Oxitriptan


Type: L-peptide linking / Mass: 220.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.5→49.7 Å / Num. obs: 54272 / % possible obs: 100 % / Redundancy: 25 % / CC1/2: 1 / Rrim(I) all: 0.108 / Net I/σ(I): 19.23
Reflection shell
Resolution (Å)Num. unique obsCC1/2Rrim(I) allDiffraction-ID
1.5-1.5986020.6661.1671
1.59-1.780940.8951
1.7-1.8475680.9681
1.84-2.0169880.9911
2.01-2.2563880.9961
2.25-2.656600.9981
2.6-3.1848470.9991
3.18-4.4938400.9991

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→49.54 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.968 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25306 2714 5 %RANDOM
Rwork0.23172 ---
obs0.23279 51557 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.625 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.46 Å2-0 Å2
3---0.91 Å2
Refinement stepCycle: 1 / Resolution: 1.5→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 22 206 2822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122687
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162523
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.6653650
X-RAY DIFFRACTIONr_angle_other_deg0.411.5745848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9755340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.067517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81910443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0570.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02587
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1162.4261360
X-RAY DIFFRACTIONr_mcbond_other2.1152.4251360
X-RAY DIFFRACTIONr_mcangle_it3.0914.3361691
X-RAY DIFFRACTIONr_mcangle_other3.0914.3381692
X-RAY DIFFRACTIONr_scbond_it2.6872.7281327
X-RAY DIFFRACTIONr_scbond_other2.6852.7251326
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1034.8591957
X-RAY DIFFRACTIONr_long_range_B_refined5.57929.672786
X-RAY DIFFRACTIONr_long_range_B_other5.55429.462757
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 196 -
Rwork0.319 3717 -
obs--99.8 %

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