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- PDB-7s13: Crystal structure of Fab in complex with mouse CD96 dimer -

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Basic information

Entry
Database: PDB / ID: 7s13
TitleCrystal structure of Fab in complex with mouse CD96 dimer
Components
  • Fab heavy chain
  • Fab light chain
  • T-cell surface protein tactile
KeywordsIMMUNE SYSTEM / Immunoglobulin / checkpoint / antibody / complex
Function / homology
Function and homology information


negative regulation of natural killer cell cytokine production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of type II interferon production / cell-matrix adhesion / response to lipopolysaccharide / membrane / cytoplasm
Similarity search - Function
T-cell surface protein tactile / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / T-cell surface protein tactile
Similarity search - Component
Biological speciesRattus (rats)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsLee, P.S. / Barman, I. / Strop, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mabs / Year: 2021
Title: Antibody blockade of CD96 by distinct molecular mechanisms.
Authors: Lee, P.S. / Chau, B. / Barman, I. / Bee, C. / Jashnani, A. / Hogan, J.M. / Aguilar, B. / Dollinger, G. / Rajpal, A. / Strop, P.
History
DepositionAug 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 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
H: Fab heavy chain
L: Fab light chain
I: Fab heavy chain
M: Fab light chain
C: T-cell surface protein tactile
D: T-cell surface protein tactile
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,57612
Polymers123,7586
Non-polymers8186
Water66737
1
H: Fab heavy chain
L: Fab light chain
D: T-cell surface protein tactile
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2867
Polymers61,8793
Non-polymers4074
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Fab heavy chain
M: Fab light chain
C: T-cell surface protein tactile
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2895
Polymers61,8793
Non-polymers4102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.030, 131.250, 186.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "C" and resid 24 through 201)
d_2ens_1chain "D"
d_1ens_2(chain "H" and (resid 1 through 126 or resid 134 through 212))
d_2ens_2chain "I"
d_1ens_3(chain "L" and resid 3 through 209)
d_2ens_3chain "M"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUGLUE4 - 117
d_12ens_1NAGNAGF
d_21ens_1GLUGLUG1 - 114
d_22ens_1NAGNAGH
d_11ens_2PCAPROA1 - 129
d_12ens_2SERPROA131 - 209
d_21ens_2PCAPROC1 - 208
d_11ens_3GLUARGB1 - 208
d_21ens_3GLUARGD1 - 208

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.996875953269, 0.0631063139363, 0.0474965991936), (-0.0534283574208, -0.981673792978, 0.182926145761), (0.0581699614655, 0.179817010655, 0.981978664871)131.296330345, -29.3968167798, 0.0638630938572
2given(-0.993168002393, -0.101609716423, -0.0573827896805), (0.0975651115782, -0.992808777982, 0.0693669904491), (-0.0640184975286, 0.0632945170585, 0.995939474107)133.703898214, -32.858799715, 3.97877101909
3given(-0.99636978713, -0.0849897265863, 0.00489833333356), (0.0850675415722, -0.991763165497, 0.0957566547776), (-0.00328034533581, 0.0958257269115, 0.995392721189)130.097602811, -33.5921600392, 0.590525790543

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Components

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Antibody , 2 types, 4 molecules HILM

#1: Antibody Fab heavy chain


Mass: 24238.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus (rats) / Production host: Homo sapiens (human)
#2: Antibody Fab light chain


Mass: 23393.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus (rats) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 4 molecules CD

#3: Protein T-cell surface protein tactile / Cell surface antigen CD96 / T cell-activated increased late expression protein


Mass: 14246.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd96 / Production host: Homo sapiens (human) / References: UniProt: Q3U0X8
#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.: 2 / Source method: obtained synthetically / 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, 41 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium citrate tribasic dihydrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→107.4 Å / Num. obs: 49907 / % possible obs: 93.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 44.12 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.049 / Net I/σ(I): 9.8
Reflection shellResolution: 2.12→2.37 Å / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2495 / CC1/2: 0.676 / Rpim(I) all: 0.364

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AIZ, 1NC2, 6ARQ

4aiz

1nc2

6arq


Resolution: 2.12→40.77 Å / SU ML: 0.3295 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.5543
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2645 2465 4.94 %
Rwork0.2166 47442 -
obs0.219 49907 67.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.65 Å2
Refinement stepCycle: LAST / Resolution: 2.12→40.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8184 0 53 37 8274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00958427
X-RAY DIFFRACTIONf_angle_d1.247111495
X-RAY DIFFRACTIONf_chiral_restr0.06941331
X-RAY DIFFRACTIONf_plane_restr0.00921449
X-RAY DIFFRACTIONf_dihedral_angle_d16.59473032
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DX-RAY DIFFRACTIONTorsion NCS5.29485331886
ens_2d_2IX-RAY DIFFRACTIONTorsion NCS1.25721460101
ens_3d_2MX-RAY DIFFRACTIONTorsion NCS1.33318559667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.160.3309160.3185194X-RAY DIFFRACTION5.17
2.16-2.20.3216110.3003295X-RAY DIFFRACTION7.7
2.2-2.240.4413150.3121364X-RAY DIFFRACTION10.4
2.26-2.30.3736230.3376493X-RAY DIFFRACTION14.72
2.3-2.360.343510.3024778X-RAY DIFFRACTION20.37
2.36-2.420.3632700.32441455X-RAY DIFFRACTION37.88
2.42-2.490.36151240.32282397X-RAY DIFFRACTION61.73
2.49-2.580.34451370.32192858X-RAY DIFFRACTION73.46
2.58-2.670.34331670.32523238X-RAY DIFFRACTION83.72
2.67-2.770.34772150.32923698X-RAY DIFFRACTION96.12
2.77-2.90.33252150.29733866X-RAY DIFFRACTION99.76
2.9-3.050.30072190.28293900X-RAY DIFFRACTION99.98
3.05-3.240.35441740.27073918X-RAY DIFFRACTION99.95
3.24-3.490.31431840.25943928X-RAY DIFFRACTION99.95
3.49-3.850.27591890.19593939X-RAY DIFFRACTION99.98
3.85-4.40.19732070.16013975X-RAY DIFFRACTION99.88
4.4-5.540.19492300.14323964X-RAY DIFFRACTION99.93
5.55-40.770.22962180.17244182X-RAY DIFFRACTION99.59
Refinement TLS params.Method: refined / Origin x: 66.936615225 Å / Origin y: -10.4209589324 Å / Origin z: 68.3616168886 Å
111213212223313233
T0.21571561676 Å2-0.00941074442779 Å20.0442218880605 Å2-0.220344686264 Å2-0.00342074616834 Å2--0.209548689356 Å2
L0.388090571124 °2-0.4357584617 °20.0163987616481 °2-0.757955811755 °2-0.227569482631 °2--0.213703243249 °2
S-0.0350388277079 Å °-0.0247482448309 Å °0.0833309478625 Å °0.168065380045 Å °0.0375517739409 Å °-0.0510741358514 Å °-0.0346427213463 Å °0.0148855770254 Å °0.000805852878305 Å °
Refinement TLS groupSelection details: all

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