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- PDB-7s4g: Fab fragment bound to the Cter peptide of Ly6G6D -

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Basic information

Entry
Database: PDB / ID: 7s4g
TitleFab fragment bound to the Cter peptide of Ly6G6D
Components
  • Lymphocyte antigen 6 complex locus protein G6d
  • heavy chain Fab 1G4
  • light chain Fab 1G4
KeywordsSIGNALING PROTEIN / leukocyte antigen-6
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / acetylcholine receptor inhibitor activity / acetylcholine receptor signaling pathway / filopodium / external side of plasma membrane / synapse / protein-containing complex / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Lymphocyte antigen 6 complex locus protein G6d/G6f
Similarity search - Domain/homology
Lymphocyte antigen 6 complex locus protein G6d
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRouge, L. / Lupardus, P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: Mol.Cancer Ther. / Year: 2022
Title: Novel Anti-LY6G6D/CD3 T-Cell-Dependent Bispecific Antibody for the Treatment of Colorectal Cancer.
Authors: Wang, P. / Sun, L.L. / Clark, R. / Hristopoulos, M. / Chiu, C.P.C. / Dillon, M. / Lin, W. / Lo, A.A. / Chalsani, S. / Das Thakur, M. / Zimmerman Savill, K.M. / Rouge, L. / Lupardus, P. / ...Authors: Wang, P. / Sun, L.L. / Clark, R. / Hristopoulos, M. / Chiu, C.P.C. / Dillon, M. / Lin, W. / Lo, A.A. / Chalsani, S. / Das Thakur, M. / Zimmerman Savill, K.M. / Rouge, L. / Lupardus, P. / Piskol, R. / Husain, B. / Ellerman, D. / Shivva, V. / Leong, S.R. / Ovacik, M. / Totpal, K. / Wu, Y. / Spiess, C. / Lee, G. / Leipold, D.D. / Polson, A.G.
History
DepositionSep 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: heavy chain Fab 1G4
B: light chain Fab 1G4
C: heavy chain Fab 1G4
D: light chain Fab 1G4
E: heavy chain Fab 1G4
F: light chain Fab 1G4
G: Lymphocyte antigen 6 complex locus protein G6d
I: Lymphocyte antigen 6 complex locus protein G6d
J: Lymphocyte antigen 6 complex locus protein G6d
K: Lymphocyte antigen 6 complex locus protein G6d
H: heavy chain Fab 1G4
L: light chain Fab 1G4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,39218
Polymers196,25512
Non-polymers1,1376
Water18,0691003
1
A: heavy chain Fab 1G4
B: light chain Fab 1G4
K: Lymphocyte antigen 6 complex locus protein G6d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3024
Polymers49,0643
Non-polymers2381
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-21 kcal/mol
Surface area19500 Å2
MethodPISA
2
C: heavy chain Fab 1G4
D: light chain Fab 1G4
G: Lymphocyte antigen 6 complex locus protein G6d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3945
Polymers49,0643
Non-polymers3302
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-21 kcal/mol
Surface area19750 Å2
MethodPISA
3
E: heavy chain Fab 1G4
F: light chain Fab 1G4
I: Lymphocyte antigen 6 complex locus protein G6d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3024
Polymers49,0643
Non-polymers2381
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-21 kcal/mol
Surface area19570 Å2
MethodPISA
4
J: Lymphocyte antigen 6 complex locus protein G6d
H: heavy chain Fab 1G4
L: light chain Fab 1G4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3945
Polymers49,0643
Non-polymers3302
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-23 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.286, 133.389, 100.038
Angle α, β, γ (deg.)90.000, 90.026, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein/peptide , 1 types, 4 molecules GIJK

#3: Protein/peptide
Lymphocyte antigen 6 complex locus protein G6d / Protein Ly6-D / Megakaryocyte-enhanced gene transcript 1 protein


Mass: 1015.120 Da / Num. of mol.: 4 / Fragment: C-ter peptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LY6G6D, C6orf23, G6D, MEGT1, NG25 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O95868

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Antibody , 2 types, 8 molecules ACEHBDFL

#1: Antibody
heavy chain Fab 1G4


Mass: 24113.111 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody
light chain Fab 1G4


Mass: 23935.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 1009 molecules

#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1003 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES pH 7, 15% PEG4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→38.82 Å / Num. obs: 90064 / % possible obs: 97.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 29.05 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 10.2
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 1.109 / Num. unique obs: 8758

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVE

1fve


Resolution: 2.2→35.05 Å / SU ML: 0.2668 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.7409
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2348 4245 4.76 %
Rwork0.192 84985 -
obs0.194 89230 96.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.48 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13283 0 72 1003 14358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011713655
X-RAY DIFFRACTIONf_angle_d1.170518565
X-RAY DIFFRACTIONf_chiral_restr0.07462088
X-RAY DIFFRACTIONf_plane_restr0.00612361
X-RAY DIFFRACTIONf_dihedral_angle_d14.94484919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.29611070.25192677X-RAY DIFFRACTION90.24
2.23-2.250.30991610.2482823X-RAY DIFFRACTION97.23
2.25-2.280.29091640.24822826X-RAY DIFFRACTION98.58
2.28-2.310.29981610.26612786X-RAY DIFFRACTION95.81
2.31-2.340.34161470.25762825X-RAY DIFFRACTION97.92
2.34-2.370.3131540.24472810X-RAY DIFFRACTION97.85
2.37-2.40.26831450.23332840X-RAY DIFFRACTION96.7
2.4-2.440.26191370.2332882X-RAY DIFFRACTION98.24
2.44-2.480.31671260.23152827X-RAY DIFFRACTION96.38
2.48-2.520.2521120.22062839X-RAY DIFFRACTION97.94
2.52-2.560.2871500.22132665X-RAY DIFFRACTION91.19
2.56-2.610.2761240.22232809X-RAY DIFFRACTION96.7
2.61-2.660.29491250.23042886X-RAY DIFFRACTION97.92
2.66-2.710.31021570.22062871X-RAY DIFFRACTION98.57
2.71-2.770.28881830.21952833X-RAY DIFFRACTION97.73
2.77-2.840.26081510.21732848X-RAY DIFFRACTION98.72
2.84-2.910.25521580.21262820X-RAY DIFFRACTION97.32
2.91-2.990.24921210.20552867X-RAY DIFFRACTION98.13
2.99-3.070.26341230.20122856X-RAY DIFFRACTION97.54
3.07-3.170.25521510.20012697X-RAY DIFFRACTION92.02
3.17-3.290.25221440.19392900X-RAY DIFFRACTION98.48
3.29-3.420.18961450.18592849X-RAY DIFFRACTION98.45
3.42-3.570.2321530.17562874X-RAY DIFFRACTION98.7
3.57-3.760.22791490.17522858X-RAY DIFFRACTION98.24
3.76-40.16151450.17082855X-RAY DIFFRACTION97.43
4-4.30.19011380.152790X-RAY DIFFRACTION94.63
4.3-4.740.1461280.1332921X-RAY DIFFRACTION99.32
4.74-5.420.1711240.14452887X-RAY DIFFRACTION97.92
5.42-6.820.22241350.18952850X-RAY DIFFRACTION95.92
6.82-35.050.22761270.18652914X-RAY DIFFRACTION96.69

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