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- PDB-5tzu: Crystal structure of human CD47 ECD bound to Fab of B6H12.2 -

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Basic information

Entry
Database: PDB / ID: 5tzu
TitleCrystal structure of human CD47 ECD bound to Fab of B6H12.2
Components
  • Heavy Chain of Fab B6H12.2
  • Leukocyte surface antigen CD47
  • Light Chain of Fab B6H12.2
KeywordsIMMUNE SYSTEM / antigen-Fab complex / immunoglobulin
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 / ATP export / cell-cell adhesion mediator activity / 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 / ATP export / cell-cell adhesion mediator activity / 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 / cellular response to type II interferon / positive regulation of inflammatory response / 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
ACETATE ION / Leukocyte surface antigen CD47
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsCardoso, R.M.F.
CitationJournal: Blood Cancer J / Year: 2017
Title: Anti-leukemic activity and tolerability of anti-human CD47 monoclonal antibodies.
Authors: Pietsch, E.C. / Dong, J. / Cardoso, R. / Zhang, X. / Chin, D. / Hawkins, R. / Dinh, T. / Zhou, M. / Strake, B. / Feng, P.H. / Rocca, M. / Santos, C.D. / Shan, X. / Danet-Desnoyers, G. / Shi, ...Authors: Pietsch, E.C. / Dong, J. / Cardoso, R. / Zhang, X. / Chin, D. / Hawkins, R. / Dinh, T. / Zhou, M. / Strake, B. / Feng, P.H. / Rocca, M. / Santos, C.D. / Shan, X. / Danet-Desnoyers, G. / Shi, F. / Kaiser, E. / Millar, H.J. / Fenton, S. / Swanson, R. / Nemeth, J.A. / Attar, R.M.
History
DepositionNov 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Light Chain of Fab B6H12.2
H: Heavy Chain of Fab B6H12.2
C: Leukocyte surface antigen CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,16014
Polymers62,3353
Non-polymers2,82611
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-8 kcal/mol
Surface area24190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.763, 54.527, 83.494
Angle α, β, γ (deg.)90.00, 95.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-458-

HOH

21H-521-

HOH

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Components

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Antibody , 3 types, 3 molecules LHC

#1: Antibody Light Chain of Fab B6H12.2


Mass: 23373.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Heavy Chain of Fab B6H12.2


Mass: 24196.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Leukocyte surface antigen CD47 / Antigenic surface determinant protein OA3 / Integrin-associated protein / IAP / Protein MER6


Mass: 14764.539 Da / Num. of mol.: 1 / Fragment: extracellular domain, UNP residues 19-141 / Mutation: C15G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD47, MER6 / Cell line (production host): HEK293(GnTI-) / Production host: Homo sapiens (human) / References: UniProt: Q08722

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Sugars , 4 types, 5 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#9: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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

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Non-polymers , 4 types, 339 molecules

#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

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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: 2.94 Å3/Da / Density % sol: 58.14 % / Mosaicity: 1.157 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2.4M ammonium sulfate, 0.1M sodium acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→37.757 Å / Num. obs: 42025 / % possible obs: 98.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 25.44 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 9.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3 % / Rmerge(I) obs: 0.368 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACT3.2data extraction
HKL-2000data scaling
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→37.76 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.26
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2129 5.07 %Random selection
Rwork0.177 ---
obs0.179 41993 98.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4029 0 184 333 4546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054321
X-RAY DIFFRACTIONf_angle_d0.8635911
X-RAY DIFFRACTIONf_dihedral_angle_d13.1812541
X-RAY DIFFRACTIONf_chiral_restr0.052715
X-RAY DIFFRACTIONf_plane_restr0.005736
LS refinement shellResolution: 2.1→2.1486 Å
RfactorNum. reflection% reflection
Rfree0.294 137 -
Rwork0.2378 2568 -
obs--97 %
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)
19.1863-4.20577.97686.5425-4.91992.00670.35250.0845-0.6650.07420.10460.2450.27190.0184-0.45520.2881-0.03220.03440.2933-0.01520.1805-36.4687-17.159522.7822
24.7548-0.08370.90714.1054-0.42926.4750.074-0.1410.02960.0728-0.00890.1917-0.0644-0.3633-0.0360.1236-0.0072-0.030.2384-0.00320.1456-32.6897-8.425728.4195
31.6645-0.37130.58971.03631.39636.62030.07210.26750.141-0.0341-0.11690.006-0.0583-0.07550.04980.1285-0.0251-0.03320.3150.00030.2295-31.7982-13.32420.0233
48.034-3.2292-2.11043.36471.61152.6237-0.06860.1462-0.09940.091-0.0125-0.06010.2477-0.42210.06160.2174-0.048-0.04020.3634-0.02750.1828-20.5501-26.8962-4.8485
52.15472.46433.46116.67645.78886.64590.1999-0.0529-0.96250.01380.1955-0.2220.7264-0.6127-0.38940.5194-0.19-0.05680.38960.02720.5119-22.3166-35.4463-1.7849
62.0007-6.4446-9.23062.00069.82042.00140.42850.17630.2308-0.1928-0.3116-0.4046-0.5238-0.2876-0.12420.24290.0109-0.01350.47640.04320.245-29.784-14.29415.4711
78.2539-2.6608-1.1763.29762.0323.29830.04080.8317-0.8734-0.0187-0.36270.30960.1927-0.61990.320.2895-0.1104-0.03110.4179-0.09460.3358-22.4862-32.2837-9.0071
80.826-0.7505-0.98395.73312.95513.01430.0198-0.0580.1568-0.3570.071-0.2439-0.1020.1918-0.08880.1524-0.0116-0.03160.28570.04860.1259-9.0168-8.192927.3003
92.7664-0.03580.98884.6552.91417.01920.0222-0.4011-0.18560.2189-0.0356-0.02820.5515-0.09830.00570.10850.0139-0.00290.25770.04820.1525-12.6291-13.926135.3949
100.7552-0.347-0.61064.88383.58194.1965-0.04720.0943-0.01070.11730.0374-0.195-0.00350.30580.0020.1156-0.0109-0.01290.27690.06780.1469-11.7074-10.298828.6952
114.4605-1.41172.0963.5034-2.39738.2977-0.00920.03530.0712-0.14920.07880.1169-0.0294-0.1663-0.05670.1281-0.00360.00760.2134-0.03390.1589-10.8082-17.89870.2637
122.0051-9.4652-7.95437.36066.78538.5614-0.7348-1.1968-0.13260.59040.77650.11650.43160.4778-0.05060.23930.039500.4484-0.01220.3282-30.0011-3.510660.1476
139.54131.99981.99922.00072.00012.00060.2596-0.27260.7367-0.51180.2549-0.9252-0.85610.7381-0.52730.2587-0.01140.04810.3334-0.02850.2522-36.930611.117162.3856
144.6583-0.6778-2.88712.29160.27194.5891-0.16860.0679-0.0120.0898-0.03120.0260.26940.05290.20550.14860.0201-0.00490.26220.00310.1398-25.8142-1.300748.655
158.9001-1.9053-8.52585.2694-0.17798.99010.10420.99070.1443-0.266-0.1750.2121-0.3308-1.11160.05220.22260.0482-0.05750.3866-0.0190.1566-32.23324.356842.3166
162.3982-0.3968-3.43723.46340.91026.0843-0.0322-0.00760.35380.0133-0.03460.2579-0.4757-0.4340.07680.23720.0422-0.00650.2294-0.00430.1906-34.41877.642552.2688
172.0025-5.9997-9.15966.53267.24519.06760.04830.373-0.1860.0807-0.05520.01590.1299-0.41880.01290.16830.0226-0.05170.36850.00050.2111-29.0137-5.058248.9571
182.0032-9.67791.99382.00241.99941.9994-0.7934-0.2613-0.62631.10210.10050.87260.8199-0.21770.73470.3413-0.04810.12810.3621-0.00380.3151-36.8581-1.748359.4157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'L' AND (RESID 1 THROUGH 18 )
2X-RAY DIFFRACTION2CHAIN 'L' AND (RESID 19 THROUGH 75 )
3X-RAY DIFFRACTION3CHAIN 'L' AND (RESID 76 THROUGH 113 )
4X-RAY DIFFRACTION4CHAIN 'L' AND (RESID 114 THROUGH 150 )
5X-RAY DIFFRACTION5CHAIN 'L' AND (RESID 151 THROUGH 163 )
6X-RAY DIFFRACTION6CHAIN 'L' AND (RESID 164 THROUGH 174 )
7X-RAY DIFFRACTION7CHAIN 'L' AND (RESID 175 THROUGH 213 )
8X-RAY DIFFRACTION8CHAIN 'H' AND (RESID 1 THROUGH 39 )
9X-RAY DIFFRACTION9CHAIN 'H' AND (RESID 40 THROUGH 73 )
10X-RAY DIFFRACTION10CHAIN 'H' AND (RESID 74 THROUGH 114 )
11X-RAY DIFFRACTION11CHAIN 'H' AND (RESID 115 THROUGH 220 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 1 THROUGH 12 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 13 THROUGH 21 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 22 THROUGH 44 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 45 THROUGH 58 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 59 THROUGH 91 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 92 THROUGH 103 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 104 THROUGH 115 )

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