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- PDB-7um3: Crystal structure of a Fab in complex with a peptide derived from... -

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Basic information

Entry
Database: PDB / ID: 7um3
TitleCrystal structure of a Fab in complex with a peptide derived from the LAG-3 D1 domain loop insertion
Components
  • D1 domain loop peptide from Lymphocyte activation gene 3 protein
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / Antibody binding fragment / Fab / LAG-3 / Relatlimab
Function / homology
Function and homology information


plasmacytoid dendritic cell activation / negative regulation of regulatory T cell differentiation / positive regulation of natural killer cell mediated cytotoxicity / MHC class II protein binding / negative regulation of interleukin-2 production / natural killer cell mediated cytotoxicity / regulation of immune response / antigen binding / MHC class II antigen presentation / T cell activation ...plasmacytoid dendritic cell activation / negative regulation of regulatory T cell differentiation / positive regulation of natural killer cell mediated cytotoxicity / MHC class II protein binding / negative regulation of interleukin-2 production / natural killer cell mediated cytotoxicity / regulation of immune response / antigen binding / MHC class II antigen presentation / T cell activation / transmembrane signaling receptor activity / adaptive immune response / cell surface receptor signaling pathway / innate immune response / external side of plasma membrane / cell surface / extracellular region / plasma membrane
Similarity search - Function
Interleukin-1 receptor family / 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
Lymphocyte activation gene 3 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3983 Å
AuthorsZorn, J.A. / Lee, P.S. / Rajpal, A. / Strop, P.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Cancer Immunol Res / Year: 2022
Title: Preclinical Characterization of Relatlimab, a Human LAG-3-Blocking Antibody, Alone or in Combination with Nivolumab.
Authors: Thudium, K. / Selby, M. / Zorn, J.A. / Rak, G. / Wang, X.T. / Bunch, R.T. / Hogan, J.M. / Strop, P. / Korman, A.J.
History
DepositionApr 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Fab heavy chain
M: Fab light chain
H: Fab heavy chain
L: Fab light chain
B: D1 domain loop peptide from Lymphocyte activation gene 3 protein
A: D1 domain loop peptide from Lymphocyte activation gene 3 protein


Theoretical massNumber of molelcules
Total (without water)100,1936
Polymers100,1936
Non-polymers00
Water5,224290
1
I: Fab heavy chain
M: Fab light chain
B: D1 domain loop peptide from Lymphocyte activation gene 3 protein


Theoretical massNumber of molelcules
Total (without water)50,0973
Polymers50,0973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-32 kcal/mol
Surface area19610 Å2
MethodPISA
2
H: Fab heavy chain
L: Fab light chain
A: D1 domain loop peptide from Lymphocyte activation gene 3 protein


Theoretical massNumber of molelcules
Total (without water)50,0973
Polymers50,0973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-29 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.238, 112.620, 125.619
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-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYPROPRO(chain 'A' and resid 83 through 94)AF83 - 942 - 13
211GLYGLYPROPROchain 'B'BE83 - 942 - 13
112VALVALTYRTYR(chain 'H' and (resid 2 through 26 or (resid 29...HC2 - 252 - 25
122PHEPHEPHEPHE(chain 'H' and (resid 2 through 26 or (resid 29...HC29 - 7829 - 78
132LEULEUSERSER(chain 'H' and (resid 2 through 26 or (resid 29...HC80 - 12880 - 135
142GLYGLYSERSER(chain 'H' and (resid 2 through 26 or (resid 29...HC134 - 215141 - 222
212VALVALTYRTYR(chain 'I' and (resid 2 through 78 or resid 80 through 215))IA2 - 252 - 25
222PHEPHEPHEPHE(chain 'I' and (resid 2 through 78 or resid 80 through 215))IA29 - 7829 - 78
232LEULEUSERSER(chain 'I' and (resid 2 through 78 or resid 80 through 215))IA80 - 12880 - 135
242GLYGLYSERSER(chain 'I' and (resid 2 through 78 or resid 80 through 215))IA134 - 215141 - 222
113GLUGLUSERSER(chain 'L' and (resid 1 through 64 or resid 66 through 213))LD1 - 631 - 63
123GLYGLYGLUGLU(chain 'L' and (resid 1 through 64 or resid 66 through 213))LD66 - 21366 - 213
213GLUGLUSERSER(chain 'M' and (resid 1 through 64 or resid 66 through 213))MB1 - 631 - 63
223GLYGLYGLUGLU(chain 'M' and (resid 1 through 64 or resid 66 through 213))MB66 - 21366 - 213

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Fab heavy chain


Mass: 24991.748 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 Fab light chain


Mass: 23434.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide D1 domain loop peptide from Lymphocyte activation gene 3 protein


Mass: 1669.863 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P18627
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris, pH 5.5, 25% PEG3350

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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 EIGER X 9M / Detector: PIXEL / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3983→83.8547 Å / Num. obs: 36288 / % possible obs: 99.51 % / Redundancy: 6.3 % / Biso Wilson estimate: 41.17 Å2 / CC1/2: 0.86 / Net I/σ(I): 6
Reflection shellResolution: 2.4→2.46 Å / Num. unique obs: 2480 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4nm4

4nm4


Resolution: 2.3983→83.8547 Å / SU ML: 0.3346 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.554
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2649 1795 4.95 %
Rwork0.2058 34493 -
obs0.2088 36288 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.36 Å2
Refinement stepCycle: LAST / Resolution: 2.3983→83.8547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6685 0 0 290 6975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00886861
X-RAY DIFFRACTIONf_angle_d1.05399369
X-RAY DIFFRACTIONf_chiral_restr0.05621050
X-RAY DIFFRACTIONf_plane_restr0.0071204
X-RAY DIFFRACTIONf_dihedral_angle_d16.59612421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.32291330.24962480X-RAY DIFFRACTION94.54
2.46-2.540.32311260.25372609X-RAY DIFFRACTION99.96
2.54-2.620.30541230.25122664X-RAY DIFFRACTION100
2.62-2.710.32041390.25752617X-RAY DIFFRACTION99.96
2.71-2.820.37191160.26672665X-RAY DIFFRACTION99.93
2.82-2.950.32511460.27242630X-RAY DIFFRACTION99.96
2.95-3.10.35351420.25272614X-RAY DIFFRACTION99.96
3.1-3.30.2961550.24442635X-RAY DIFFRACTION100
3.3-3.550.30121420.2332661X-RAY DIFFRACTION99.96
3.55-3.910.25911460.19412668X-RAY DIFFRACTION99.93
3.91-4.480.20221240.16172698X-RAY DIFFRACTION99.72
4.48-5.640.1941530.14652716X-RAY DIFFRACTION100
5.64-56.310.21981500.17322836X-RAY DIFFRACTION99.67

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