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- PDB-8rp8: Structure of K2 Fab in complex with human CD47 ECD -

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Basic information

Entry
Database: PDB / ID: 8rp8
TitleStructure of K2 Fab in complex with human CD47 ECD
Components
  • K2 Fab heavy chain
  • K2 Fab light chain
  • Leukocyte surface antigen CD47
KeywordsIMMUNE SYSTEM / Fab / glycoprotein
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 / regulation of interleukin-10 production / positive regulation of cell-cell adhesion / ATP export / 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 / regulation of interleukin-10 production / positive regulation of cell-cell adhesion / ATP export / regulation of tumor necrosis factor production / regulation of interleukin-12 production / regulation of nitric oxide biosynthetic process / regulation of interleukin-6 production / negative regulation of phagocytosis / Signal regulatory protein family interactions / thrombospondin receptor activity / tertiary granule membrane / cellular response to interleukin-1 / Integrin cell surface interactions / 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 / positive regulation of cell population proliferation / Neutrophil degranulation / apoptotic process / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Leukocyte surface antigen CD47
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLaursen, M. / Kelpsas, V. / Rose, N.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Other private Switzerland
CitationJournal: Mabs / Year: 2024
Title: Structural analysis of light chain-driven bispecific antibodies targeting CD47 and PD-L1.
Authors: Malinge, P. / Chauchet, X. / Bourguignon, J. / Bosson, N. / Calloud, S. / Bautzova, T. / Borlet, M. / Laursen, M. / Kelpsas, V. / Rose, N. / Gueneau, F. / Ravn, U. / Magistrelli, G. / Fischer, N.
History
DepositionJan 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: K2 Fab heavy chain
B: K2 Fab light chain
C: Leukocyte surface antigen CD47
D: Leukocyte surface antigen CD47
H: K2 Fab heavy chain
L: K2 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,09916
Polymers123,3766
Non-polymers1,72410
Water14,736818
1
A: K2 Fab heavy chain
B: K2 Fab light chain
C: Leukocyte surface antigen CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5508
Polymers61,6883
Non-polymers8625
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Leukocyte surface antigen CD47
H: K2 Fab heavy chain
L: K2 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5508
Polymers61,6883
Non-polymers8625
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.415, 71.812, 78.379
Angle α, β, γ (deg.)109.45, 95.55, 118.9
Int Tables number1
Space group name H-MP1

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Components

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Antibody , 2 types, 4 molecules AHBL

#1: Antibody K2 Fab heavy chain


Mass: 23468.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody K2 Fab light chain


Mass: 23472.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 8 molecules CD

#3: Protein Leukocyte surface antigen CD47 / Antigenic surface determinant protein OA3 / Integrin-associated protein / IAP / Protein MER6


Mass: 14747.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD47, MER6 / Production host: Homo sapiens (human) / References: UniProt: Q08722
#6: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: isolated from a natural 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 , 3 types, 822 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 818 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M sodium citrate, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2021
RadiationMonochromator: Si(111) HDCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→70.22 Å / Num. obs: 78163 / % possible obs: 97.4 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.022 / Rrim(I) all: 0.043 / Χ2: 0.97 / Net I/σ(I): 19.2
Reflection shellResolution: 2→2.04 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 7.5 / Num. unique obs: 4427 / CC1/2: 0.981 / Rpim(I) all: 0.089 / Rrim(I) all: 0.171 / Χ2: 1.07 / % possible all: 96.8

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
PHASER2.8.3phasing
Coot0.9.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20.06 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.173 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.149 / SU Rfree Cruickshank DPI: 0.149
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 3862 -RANDOM
Rwork0.1803 ---
obs0.182 78096 97.4 %-
Displacement parametersBiso mean: 37.02 Å2
Baniso -1Baniso -2Baniso -3
1-3.665 Å22.0127 Å2-0.0078 Å2
2--2.7906 Å2-2.6098 Å2
3----6.4555 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2→20.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8294 0 110 818 9222
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088688HARMONIC2
X-RAY DIFFRACTIONt_angle_deg111825HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2953SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1472HARMONIC5
X-RAY DIFFRACTIONt_it8688HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1174SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7759SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.91
X-RAY DIFFRACTIONt_other_torsion14.31
LS refinement shellResolution: 2→2.01 Å
RfactorNum. reflection% reflection
Rfree0.2226 73 -
Rwork0.1918 --
obs0.1932 1562 96.31 %
Refinement TLS params.

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)
12.23350.8448-0.02770.57620.01320.23590.02990.15420.15040.1542-0.03420.03390.15040.03390.0043-0.01850.0511-0.0433-0.00580.0271-0.049419.9396-47.344833.1741
21.071-0.28840.11840.3745-0.04260.0711-0.05640.00510.10640.00510.0182-0.03540.1064-0.03540.0383-0.03760.0076-0.008-0.02670.00790.034620.1452-34.380220.3934
31.24722.13850.24116.08780.66280.5250.0590.1733-0.05020.1733-0.0127-0.0241-0.0502-0.0241-0.0464-0.0505-0.03320.0032-0.06160.01320.0023-18.9697-65.934726.0913
40.9561-1.479-0.13784.90280.31640.42570.0319-0.19530.0552-0.1953-0.01180.00580.05520.0058-0.0202-0.02830.0341-0.0139-0.04280.0041-0.026-18.91581.3737-7.2431
51.8218-0.30330.04610.320.05330.2525-0.0626-0.1017-0.169-0.10170.07880.0225-0.1690.0225-0.0163-0.0095-0.07550.03730.00050.0029-0.065320.0303-16.9747-14.2
60.83560.318-0.06610.4335-0.0443-0.0096-0.04850.0112-0.11940.01120.0202-0.0479-0.1194-0.04790.0283-0.0454-0.0090.0081-0.02180.00640.041620.0576-30.086-1.5116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 217
2X-RAY DIFFRACTION2{ B|* }B1 - 214
3X-RAY DIFFRACTION2{ B|* }B301 - 302
4X-RAY DIFFRACTION3{ C|* }C1 - 118
5X-RAY DIFFRACTION3{ C|* }C201 - 203
6X-RAY DIFFRACTION4{ D|* }D1 - 118
7X-RAY DIFFRACTION4{ D|* }D201 - 203
8X-RAY DIFFRACTION5{ H|* }H1 - 217
9X-RAY DIFFRACTION6{ L|* }L1 - 214
10X-RAY DIFFRACTION6{ L|* }L301 - 302

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