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- PDB-6txz: FAB PART OF M6903 IN COMPLEX WITH HUMAN TIM3 -

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Basic information

Entry
Database: PDB / ID: 6txz
TitleFAB PART OF M6903 IN COMPLEX WITH HUMAN TIM3
Components
  • Fab H
  • Fab L
  • Hepatitis A virus cellular receptor 2
KeywordsIMMUNE SYSTEM / FAB / ANTIBODY / TIM3
Function / homology
Function and homology information


regulation of tolerance induction dependent upon immune response / negative regulation of interleukin-3 production / negative regulation of granulocyte colony-stimulating factor production / negative regulation of myeloid dendritic cell activation / Interleukin-2 family signaling / negative regulation of interferon-alpha production / negative regulation of T-helper 1 type immune response / negative regulation of defense response to bacterium / toll-like receptor 7 signaling pathway / natural killer cell tolerance induction ...regulation of tolerance induction dependent upon immune response / negative regulation of interleukin-3 production / negative regulation of granulocyte colony-stimulating factor production / negative regulation of myeloid dendritic cell activation / Interleukin-2 family signaling / negative regulation of interferon-alpha production / negative regulation of T-helper 1 type immune response / negative regulation of defense response to bacterium / toll-like receptor 7 signaling pathway / natural killer cell tolerance induction / negative regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of defense response to bacterium / negative regulation of immunological synapse formation / toll-like receptor 3 signaling pathway / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / positive regulation of interleukin-1 production / toll-like receptor 9 signaling pathway / mediator complex / positive regulation of macrophage activation / macrophage activation involved in immune response / anchoring junction / negative regulation of interleukin-2 production / negative regulation of NF-kappaB transcription factor activity / positive regulation of interleukin-4 production / negative regulation of interleukin-6 production / negative regulation of type II interferon production / immunological synapse / negative regulation of tumor necrosis factor production / maternal process involved in female pregnancy / positive regulation of chemokine production / negative regulation of T cell proliferation / positive regulation of T cell proliferation / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / cellular response to lipopolysaccharide / adaptive immune response / early endosome / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / negative regulation of gene expression / innate immune response / regulation of transcription by RNA polymerase II / cell surface / metal ion binding / plasma membrane
Similarity search - Function
: / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins ...: / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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
Hepatitis A virus cellular receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsMusil, D. / Sood, V.
CitationJournal: Oncoimmunology / Year: 2020
Title: Identification and characterization of M6903, an antagonistic anti-TIM-3 monoclonal antibody.
Authors: Zhang, D. / Jiang, F. / Zaynagetdinov, R. / Huang, H. / Sood, V.D. / Wang, H. / Zhao, X. / Jenkins, M.H. / Ji, Q. / Wang, Y. / Nannemann, D.P. / Musil, D. / Wesolowski, J. / Paoletti, A. / ...Authors: Zhang, D. / Jiang, F. / Zaynagetdinov, R. / Huang, H. / Sood, V.D. / Wang, H. / Zhao, X. / Jenkins, M.H. / Ji, Q. / Wang, Y. / Nannemann, D.P. / Musil, D. / Wesolowski, J. / Paoletti, A. / Bartholomew, T. / Derner, M.G. / An, Q. / Iffland, C. / Halle, J.P.
History
DepositionJan 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 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
A: Hepatitis A virus cellular receptor 2
B: Hepatitis A virus cellular receptor 2
C: Hepatitis A virus cellular receptor 2
D: Hepatitis A virus cellular receptor 2
H: Fab H
I: Fab H
J: Fab H
K: Fab H
L: Fab L
M: Fab L
N: Fab L
O: Fab L


Theoretical massNumber of molelcules
Total (without water)236,80812
Polymers236,80812
Non-polymers00
Water00
1
A: Hepatitis A virus cellular receptor 2
H: Fab H
L: Fab L


Theoretical massNumber of molelcules
Total (without water)59,2023
Polymers59,2023
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-32 kcal/mol
Surface area23850 Å2
MethodPISA
2
B: Hepatitis A virus cellular receptor 2
I: Fab H
M: Fab L


Theoretical massNumber of molelcules
Total (without water)59,2023
Polymers59,2023
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-33 kcal/mol
Surface area23970 Å2
MethodPISA
3
C: Hepatitis A virus cellular receptor 2
J: Fab H
N: Fab L


Theoretical massNumber of molelcules
Total (without water)59,2023
Polymers59,2023
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-35 kcal/mol
Surface area23890 Å2
MethodPISA
4
D: Hepatitis A virus cellular receptor 2
K: Fab H
O: Fab L


Theoretical massNumber of molelcules
Total (without water)59,2023
Polymers59,2023
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-34 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.350, 270.115, 197.889
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Hepatitis A virus cellular receptor 2 / HAVcr-2 / T-cell immunoglobulin and mucin domain-containing protein 3 / TIMD-3 / T-cell ...HAVcr-2 / T-cell immunoglobulin and mucin domain-containing protein 3 / TIMD-3 / T-cell immunoglobulin mucin receptor 3 / TIM-3 / T-cell membrane protein 3


Mass: 12429.196 Da / Num. of mol.: 4 / Fragment: FAB ANTIBODY FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HAVCR2, TIM3, TIMD3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TDQ0
#2: Antibody
Fab H


Mass: 24224.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody
Fab L


Mass: 22548.859 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 3.37 Å3/Da / Density % sol: 63.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% (v/v) PEG400, 0.1 M Tris HCL pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.06→48.6 Å / Num. obs: 59975 / % possible obs: 99 % / Redundancy: 3.814 % / Biso Wilson estimate: 97.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.087 / Χ2: 0.972 / Net I/σ(I): 15.36 / Num. measured all: 228723 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.06-3.313.8650.5022.954694812558121460.8050.58396.7
3.31-3.653.8060.2226.334589212074120580.9510.25999.9
3.65-4.193.7550.10112.334502812054119900.9890.11799.5
4.19-5.113.9410.04923.324162710577105620.9970.05799.9
5.11-6.483.8250.04325.4825416666066440.9970.05199.8
6.48-8.323.60.03330.4512333344034260.9980.03999.6
8.32-12.143.7050.02344.427803213321060.9990.02798.7
12.14-19.433.6410.02245.6728587957850.9990.02698.7
19.43-48.63.1710.01847.068182862580.9990.02290.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F71

5f71


Resolution: 3.06→48.6 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.388
RfactorNum. reflection% reflectionSelection details
Rfree0.253 523 0.87 %RANDOM
Rwork0.197 ---
obs0.197 59973 99.1 %-
Displacement parametersBiso max: 172.92 Å2 / Biso mean: 80.01 Å2 / Biso min: 34.48 Å2
Baniso -1Baniso -2Baniso -3
1-2.4075 Å20 Å20 Å2
2--3.025 Å20 Å2
3----5.4325 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 3.06→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16054 0 0 0 16054
Num. residues----2134
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5320SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2742HARMONIC5
X-RAY DIFFRACTIONt_it16475HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2155SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17139SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d16475HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg22472HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion19.57
LS refinement shellResolution: 3.06→3.11 Å / Rfactor Rfree error: 0 / Total num. of bins used: 26
RfactorNum. reflection% reflection
Rfree0.2839 24 1.04 %
Rwork0.3141 2283 -
all0.3138 2307 -
obs--87.19 %
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)
13.2012-1.9044-1.66084.61220.75511.83060.1217-0.1335-0.06960.80160.04010.93720.2204-0.1755-0.1618-0.2773-0.150.2261-0.1667-0.02530.0473-112.547-20.034821.6742
23.3824-0.72140.38214.38610.48891.3620.0447-0.220.39570.21790.1995-0.1069-0.27390.0391-0.2442-0.09740.03370.0789-0.0182-0.0352-0.0063-25.4564-37.8334-9.6632
32.36090.1776-1.23081.2195-0.51232.51890.19350.2802-0.1441-0.501-0.18310.2951-0.1261-0.0223-0.01040.05320.1513-0.0321-0.1229-0.0775-0.1363-31.7139-56.0935-30.1315
42.9805-0.73271.45581.41930.26016.3712-0.02270.28950.7765-0.1375-0.1911-0.2679-0.49440.06110.2137-0.0860.01630.1419-0.1968-0.06730.2106-34.2022-21.1979-19.7942
57.0378-3.8584-0.15686.9987-1.17043.7189-0.1754-0.30980.16770.2347-0.0266-0.2807-0.21370.45450.202-0.2038-0.0265-0.04040.014-0.0051-0.0873-72.6131-37.12073.6269
60.6523-1.05340.471.9513-0.77343.976-0.0614-0.101-0.4757-0.001-0.06040.50240.0756-0.10480.1218-0.15990.0250.0601-0.08440.10270.239-68.4781-53.5392-8.9836
72.6958-2.28511.04422.4851-1.00840.48780.20330.1450.1284-0.1335-0.1386-0.25960.13110.0811-0.0647-0.0416-0.01660.05920.0302-0.0497-0.04364.6901-66.8042-14.8354
85.7177-0.8370.7881.49910.62350.55870.12080.47780.2687-0.9836-0.187-0.0465-0.20030.21450.06620.36590.1991-0.1126-0.13490.0424-0.3672-74.9828-22.8871-36.8088
92.4006-1.5053-1.49134.26821.06932.34850.1824-0.14330.10220.2394-0.07470.6008-0.0364-0.059-0.1077-0.1975-0.1093-0.0087-0.1395-0.02480.076-102.95-10.20439.2485
102.5762-0.1925-1.80490.89110.14851.370.22090.4332-0.2305-0.4877-0.23430.1719-0.1147-0.16780.01340.17340.1833-0.1382-0.0199-0.1099-0.1901-41.9224-53.9555-44.0582
113.2948-2.00530.03862.19280.03840.7366-0.0630.05740.66590.0745-0.0126-0.7049-0.05130.10680.0757-0.1879-0.04890.0219-0.09410.01930.097417.7822-56.3163-7.2781
124.56530.52320.38693.68920.66811.41360.15340.16360.1579-0.5327-0.15580.0755-0.0737-0.07090.00240.03660.2137-0.0784-0.1559-0.0414-0.2798-76.7298-19.8478-19.8474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ N|* }N1 - 210
2X-RAY DIFFRACTION2{ A|* }A22 - 130
3X-RAY DIFFRACTION3{ O|* }O1 - 211
4X-RAY DIFFRACTION4{ B|* }B22 - 130
5X-RAY DIFFRACTION5{ C|* }C22 - 130
6X-RAY DIFFRACTION6{ D|* }D22 - 130
7X-RAY DIFFRACTION7{ H|* }H1 - 219
8X-RAY DIFFRACTION8{ I|* }I1 - 220
9X-RAY DIFFRACTION9{ J|* }J1 - 218
10X-RAY DIFFRACTION10{ K|* }K1 - 220
11X-RAY DIFFRACTION11{ L|* }L3 - 211
12X-RAY DIFFRACTION12{ M|* }M2 - 211

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