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- PDB-2vsc: Structure of the immunoglobulin-superfamily ectodomain of human CD47 -

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Basic information

Entry
Database: PDB / ID: 2vsc
TitleStructure of the immunoglobulin-superfamily ectodomain of human CD47
ComponentsLEUKOCYTE SURFACE ANTIGEN CD47
KeywordsCELL ADHESION / IMMUNOGLOBULIN DOMAIN / SIGNAL REGULATORY PROTEIN / CD47 / MEMBRANE / GLYCOPROTEIN / IMMUNOGLOBULIN SUPERFAMILY / PYRROLIDONE CARBOXYLIC ACID / TRANSMEMBRANE / PAIRED RECEPTOR / ALTERNATIVE SPLICING
Function / homology
Function and homology information


cellular response to interleukin-12 / regulation of Fc receptor mediated stimulatory signaling pathway / protein binding involved in heterotypic cell-cell adhesion / positive regulation of monocyte extravasation / regulation of type II interferon production / cell-cell adhesion mediator activity / ATP export / positive regulation of cell-cell adhesion / regulation of interleukin-10 production / regulation of tumor necrosis factor production ...cellular response to interleukin-12 / regulation of Fc receptor mediated stimulatory signaling pathway / protein binding involved in heterotypic cell-cell adhesion / positive regulation of monocyte extravasation / regulation of type II interferon production / cell-cell adhesion mediator activity / ATP export / positive regulation of cell-cell adhesion / regulation of interleukin-10 production / regulation of tumor necrosis factor production / regulation of interleukin-12 production / regulation of nitric oxide biosynthetic process / negative regulation of phagocytosis / regulation of interleukin-6 production / Signal regulatory protein family interactions / thrombospondin receptor activity / tertiary granule membrane / Integrin cell surface interactions / cellular response to interleukin-1 / specific granule membrane / positive regulation of phagocytosis / positive regulation of stress fiber assembly / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / positive regulation of inflammatory response / cellular response to type II interferon / positive regulation of T cell activation / cell migration / angiogenesis / inflammatory response / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / cell surface / extracellular exosome / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins ...Leukocyte surface antigen CD47 / CD47-like, transmembrane / CD47 immunoglobulin-like / Leukocyte surface antigen CD47, IgV / CD47 transmembrane region / CD47 immunoglobulin-like 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
Leukocyte surface antigen CD47
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHatherley, D. / Graham, S.C. / Turner, J. / Harlos, K. / Stuart, D.I. / Barclay, A.N.
CitationJournal: Mol.Cell / Year: 2008
Title: Paired Receptor Specificity Explained by Structures of Signal Regulatory Proteins Alone and Complexed with Cd47.
Authors: Hatherley, D. / Graham, S.C. / Turner, J. / Harlos, K. / Stuart, D.I. / Barclay, A.N.
History
DepositionApr 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2008Provider: 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 2.0Mar 11, 2020Group: Data collection / Other / Polymer sequence / Category: chem_comp / entity_poly / pdbx_database_status
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf
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 / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Dec 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEUKOCYTE SURFACE ANTIGEN CD47
B: LEUKOCYTE SURFACE ANTIGEN CD47
C: LEUKOCYTE SURFACE ANTIGEN CD47
D: LEUKOCYTE SURFACE ANTIGEN CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,77618
Polymers58,0734
Non-polymers2,70314
Water6,359353
1
A: LEUKOCYTE SURFACE ANTIGEN CD47
B: LEUKOCYTE SURFACE ANTIGEN CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3889
Polymers29,0372
Non-polymers1,3527
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-34.8 kcal/mol
Surface area15350 Å2
MethodPQS
2
C: LEUKOCYTE SURFACE ANTIGEN CD47
D: LEUKOCYTE SURFACE ANTIGEN CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3889
Polymers29,0372
Non-polymers1,3527
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-33.3 kcal/mol
Surface area15230 Å2
MethodPQS
Unit cell
Length a, b, c (Å)201.137, 47.502, 56.811
Angle α, β, γ (deg.)90.00, 99.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2037-

HOH

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Components

#1: Antibody
LEUKOCYTE SURFACE ANTIGEN CD47 / INTEGRIN-ASSOCIATED PROTEIN / IAP / ANTIGENIC SURFACE DETERMINANT PROTEIN OA3 / PROTEIN MER6 / CD47


Mass: 14518.302 Da / Num. of mol.: 4
Fragment: IMMUNOGLOBULIN-SUPERFAMILY ECTODOMAIN, 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
#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.: 12
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE NUMBERING IS FOR MATURE PROTEIN (LACKING N- TERMINAL 18 AMINO ACID SIGNAL SEQUENCE). ...RESIDUE NUMBERING IS FOR MATURE PROTEIN (LACKING N- TERMINAL 18 AMINO ACID SIGNAL SEQUENCE). RESIDUE 1 (GLN) CYCLISES TO FORM A PYROGLUTAMIC ACID. RESIDUE 15 WAS MUTATED FROM CYS TO GLY.

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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: 2.6 Å3/Da / Density % sol: 52.5 % / Description: NONE
Crystal growpH: 5.5
Details: 200 NL 17 MG/ML CD47 PLUS 100 NL RESERVOIR (0.2 M MGCL2, 0.1 M BIS-TRIS PH 5.5, 25% W/V PEG 3350) EQUILIBRATED AGAINST 95 UL OF RESERVOIR AT 20.5 C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 12, 2006 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→28.3 Å / Num. obs: 41496 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.9 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JJS, CHAIN C

2jjs


Resolution: 1.9→28.19 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.331 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. B VALUES INCLUDE TLS CONTRIBUTIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2100 5.1 %RANDOM
Rwork0.216 ---
obs0.219 39392 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.15 Å2
2---0.76 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3647 0 170 353 4170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223916
X-RAY DIFFRACTIONr_bond_other_d0.0040.022605
X-RAY DIFFRACTIONr_angle_refined_deg1.3672.0175333
X-RAY DIFFRACTIONr_angle_other_deg0.8473.0036313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6215459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93825.155161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38115676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8531513
X-RAY DIFFRACTIONr_chiral_restr0.080.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02734
X-RAY DIFFRACTIONr_nbd_refined0.1810.2615
X-RAY DIFFRACTIONr_nbd_other0.1960.22624
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21845
X-RAY DIFFRACTIONr_nbtor_other0.1080.22087
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2303
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6211.52978
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.76923747
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.41131903
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1334.51579
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.353 139
Rwork0.249 2484
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)
17.37431.82840.44053.68830.99782.6814-0.01720.1094-0.54370.0634-0.04330.09150.1989-0.29810.0605-0.198-0.0630.0384-0.1319-0.0633-0.07125.3517-36.93620.4823
214.847417.468210.2823.252814.43879.15190.6887-0.68720.57121.5321-0.98970.62560.5558-0.52370.3010.1369-0.17320.0352-0.18320.0199-0.173726.3216-7.547541.2028
32.36652.12080.85516.10290.82272.40370.1638-0.1475-0.03880.4664-0.2482-0.1528-0.1123-0.11770.0844-0.1206-0.0652-0.0179-0.20260.0042-0.166730.4424-8.387734.3321
414.400815.26610.80621.444112.86710.5476-0.10320.7086-0.6953-0.47370.251-0.13470.0499-0.0077-0.1478-0.2332-0.08010.0906-0.0132-0.16-0.06728.2322-36.85212.5952
54.3001-1.66070.22554.2933-0.68051.71180.1450.13440.0503-0.0431-0.0968-0.0690.01080.0567-0.0482-0.17040.03440.0214-0.20420.0108-0.188242.17360.639814.0996
616.7554-18.28837.995823.0595-11.18225.9056-0.5244-0.45590.06530.76860.74450.5412-0.7255-0.702-0.22010.11110.25510.00940.03440.0304-0.141915.743631.14583.9436
79.9259-8.29213.492110.5664-5.21783.66040.5961.37240.0928-0.6637-0.59940.142-0.0342-0.03140.00340.07320.24050.01520.21970.0667-0.147419.494128.6316-2.6344
815.8131-18.01765.87821.1371-7.11844.17420.31040.73790.8698-0.4489-0.661-1.093-0.07890.12590.3506-0.11410.05950.0636-0.14020.0594-0.112744.073.73645.5193
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 100
2X-RAY DIFFRACTION1A1001 - 1100
3X-RAY DIFFRACTION2A101 - 120
4X-RAY DIFFRACTION3B1 - 100
5X-RAY DIFFRACTION3B1000 - 1100
6X-RAY DIFFRACTION4B101 - 120
7X-RAY DIFFRACTION5C1 - 100
8X-RAY DIFFRACTION5C1000 - 1100
9X-RAY DIFFRACTION6C101 - 120
10X-RAY DIFFRACTION7D1 - 100
11X-RAY DIFFRACTION8D101 - 120
12X-RAY DIFFRACTION8D1000 - 1100

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