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- PDB-8tq9: Crystal structure of Fab.S19.8 in complex with MHC-I (H2-Dd) -

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Basic information

Entry
Database: PDB / ID: 8tq9
TitleCrystal structure of Fab.S19.8 in complex with MHC-I (H2-Dd)
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Fab.S19.8 Heavy Chain
  • Fab.S19.8 Light Chain
  • H-2 class I histocompatibility antigen, D-D alpha chain
  • Transmembrane protein gp41Transmembrane protein
KeywordsIMMUNE SYSTEM / histocompatibility complex class I / MHC-I / immune response / immune system Fab / antibody / anti-MHC antibody / cancer tumor
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of membrane depolarization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of membrane depolarization / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Binding and entry of HIV virion / cellular defense response / beta-2-microglobulin binding / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / Neutrophil degranulation / host cell endosome membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / actin filament organization / lumenal side of endoplasmic reticulum membrane / peptide binding / Assembly Of The HIV Virion / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / Budding and maturation of HIV virion / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / iron ion transport / protein refolding / antibacterial humoral response / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / intracellular iron ion homeostasis / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / viral protein processing / defense response to Gram-positive bacterium / symbiont entry into host cell / immune response / virus-mediated perturbation of host defense response / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / signaling receptor binding / innate immune response / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-D alpha chain / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMus musculus (house mouse)
HIV-1 M:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJiang, J. / Boyd, L.F. / Natarajan, K. / Margulies, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J Immunol. / Year: 2024
Title: Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction.
Authors: Boyd, L.F. / Jiang, J. / Ahmad, J. / Natarajan, K. / Margulies, D.H.
History
DepositionAug 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-D alpha chain
B: Beta-2-microglobulin
H: Fab.S19.8 Heavy Chain
L: Fab.S19.8 Light Chain
P: Transmembrane protein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0617
Polymers91,8735
Non-polymers1882
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10240 Å2
ΔGint-63 kcal/mol
Surface area36240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.901, 183.181, 216.715
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein H-2 class I histocompatibility antigen, D-D alpha chain / MHC-I H2-Dd A chain


Mass: 31819.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01900
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11894.601 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01887

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Protein/peptide , 1 types, 1 molecules P

#5: Protein/peptide Transmembrane protein gp41 / Transmembrane protein / TM / Glycoprotein 41 / gp41


Mass: 1075.265 Da / Num. of mol.: 1 / Fragment: HV1: HIV-1 P18-I10 (UNP residues 311-320) / Source method: obtained synthetically / Source: (synth.) HIV-1 M:B_HXB2R (virus) / References: UniProt: P04578

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Antibody , 2 types, 2 molecules HL

#3: Antibody Fab.S19.8 Heavy Chain


Mass: 23467.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): S19.8 / Production host: Mus musculus (house mouse)
#4: Antibody Fab.S19.8 Light Chain


Mass: 23615.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): S19.8 / Production host: Mus musculus (house mouse)

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Non-polymers , 3 types, 60 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5 M ammonium sulfate, 0.1 M sodium citrate, pH 5.6, 1.0 M lithium sulfate

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→54.18 Å / Num. obs: 24406 / % possible obs: 95.4 % / Redundancy: 7.4 % / Biso Wilson estimate: 59.02 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.042 / Net I/σ(I): 7.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.8 % / Rmerge(I) obs: 1.158 / Mean I/σ(I) obs: 7.2 / Num. unique obs: 2174 / CC1/2: 0.648 / CC star: 0.887 / Rpim(I) all: 0.455 / % possible all: 89.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5WEU

5weu


Resolution: 2.9→54.18 Å / SU ML: 0.3353 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 24.1139
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2396 1186 5 %
Rwork0.187 22512 -
obs0.1897 23698 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.12 Å2
Refinement stepCycle: LAST / Resolution: 2.9→54.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6315 0 11 58 6384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00276495
X-RAY DIFFRACTIONf_angle_d0.57828853
X-RAY DIFFRACTIONf_chiral_restr0.0429960
X-RAY DIFFRACTIONf_plane_restr0.00521143
X-RAY DIFFRACTIONf_dihedral_angle_d4.517891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.36461380.28552616X-RAY DIFFRACTION90.83
3.03-3.190.34761430.25852712X-RAY DIFFRACTION93.64
3.19-3.390.28631450.22192777X-RAY DIFFRACTION95.55
3.39-3.650.26021490.19542828X-RAY DIFFRACTION96.5
3.65-4.020.241500.17852828X-RAY DIFFRACTION96.69
4.02-4.60.19671460.14692789X-RAY DIFFRACTION94.74
4.6-5.80.20911550.15212938X-RAY DIFFRACTION98.57
5.8-54.180.20661600.19163024X-RAY DIFFRACTION96.81
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)
12.212601975660.7303021431410.4186205367574.114681716231.551331415094.3918580229-0.1216817595810.0959239509976-0.0769590787155-0.3519722317380.0960014794307-0.0827235453831-0.128751016004-0.1108780572630.05267050028850.3656359458250.04019105068510.03010962302080.2617507126110.07049059861550.24154419269221.05097026375.932640700118.1772786402
22.11159527020.860014651432-1.222336714932.78332740256-0.3614472261492.29223879944-0.05041246268210.2091810638830.09277120455430.1532046275180.587571443161.04178606024-0.357117302969-1.0879019286-0.5134200179140.466060784580.1367407217920.09914141946140.6772409042360.3188039940210.647499039787-2.5414101855650.785733855224.0769521525
32.100310934721.336630955991.265864354948.325241097442.612075636912.25427047966-0.1846846467790.1898191813480.349209988453-0.1583189572470.1974024567270.582140381074-0.1833589900720.0902878779966-0.1745424017240.4832272910090.08768517674410.09847733723520.4094224342050.06969987205910.3240967191113.459482325661.801481373435.3535880331
41.66587379989-0.1062123838730.7528303835452.080432171940.6323312717641.12703263725-0.3508657602090.171437763315-0.360342813157-0.285652794240.32605184376-0.4075768548010.1711513283190.08456724249610.03830304963030.560134855875-0.02802723504090.08163318302180.3532669487810.0507338261870.32356760308217.08049998951.916767086730.2036724246
50.0174815034129-0.265417132708-0.01446843085138.87102426671-0.19341409226-0.0340213038789-0.04633178020930.0682245608381-0.367883733531-0.846201066075-0.0110019803828-0.5431183852840.416512816512-0.005510038369040.02597199495440.5147401635420.02810550436950.1308745317020.5776960552180.026683746520.49994437048620.470024286958.510360343128.9879455441
61.670536398950.9144677595711.078327157539.136340409822.882126390082.84137030232-0.132376754263-0.0918172487106-0.378968653679-0.1111882723070.0855174205303-0.2082397358350.1982037461870.1475816401230.08802023455610.4034714158960.00937610136970.1147063412150.3732732007340.1215733732430.41221981990516.580615504149.908998971235.0609055742
71.13297234752-0.01424170048950.9515905676232.22832855802-0.2565323829514.16035486-0.0607843753899-0.3053145705090.272702972025-0.062052862139-0.1074071248190.147616578435-0.509406663315-0.3879295931380.1723526801210.2922091638430.0121803452938-0.03179677649870.4456314569290.02503313604820.35722327521323.752280806272.75496814961.538626427
84.529508858810.631312895604-0.7060846281854.083984324040.986317575314.499135283420.0550497384795-0.557011551976-0.3881051598250.06103508476990.08045486782480.3075098217250.273344380408-0.59183237867-0.1029745957780.3515342086180.00330724538324-0.07637505353470.3984666412550.07906234371840.26718207467820.247170951263.104465845259.0286662256
92.42406336897-0.2999038764322.093556418211.313629164820.7049293005423.861338819360.0813516279687-0.1646036236890.03309444092720.1319247472230.0814960867385-0.090497863475-0.337053560529-0.257346853117-0.07735994220130.27017231190.0153549906939-0.01682619485030.2877338152230.0513816078420.29988215344427.125468163469.68324060665.24543884
106.385450584531.01606055852-0.03926433661793.362517732060.2935682031064.482753960860.350546106101-0.3525815052990.6405392158090.130819731912-0.221308201122-1.10853939695-0.3477456847310.200125450088-0.2542608730750.5156011427130.0264110783496-0.1565332894720.446861913631-0.05875399437240.85117096700749.119424069476.630541465284.0071399556
117.33491594689-1.166062719931.728946042463.51331910732-1.406089491925.109572927260.431763673589-0.1265086323251.364143016470.2924953026520.153702916188-0.288235880294-0.994873967874-0.195585974066-0.1940484294780.5443743031460.0461313331417-0.131445728010.476025905295-0.2019416222790.64539179011640.747871642482.853702729186.302698084
124.14194243851-1.04395283231.304259300392.69749995854-0.9457397386713.149364854010.3698327161640.335489066328-0.545953891399-0.564684501588-0.0759487344971-0.7001530486750.2731591811320.795683055239-0.2091810166390.3678720896460.1150009522990.03135250704020.609901425733-0.06432651164440.5676649916441.528839783959.374069564652.0305828051
134.04669516306-0.306327872018-0.1244326637731.901028481290.3721943314424.06689790527-0.123884310653-0.5273484927230.05945875444390.7495621476690.163076319939-0.6391185237440.3054386759080.7282932550110.09977470470980.5891562428540.0136007393845-0.267534741110.51233664284-0.006504989578990.68643683148854.092296438164.184104275386.5777145554
143.417697831420.461013597048-0.5197023307194.194977767822.315008958588.699418051940.3032232258840.521248718383-0.0754575559923-0.7178258194250.141497891946-0.87544131943-1.517716917460.95226830054-0.4386525669240.505901853644-0.0152678235510.1160951003990.6587062032670.0646814802540.43676468308725.298949987181.983056813115.9896229367
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 174 )AA2 - 1741 - 173
22chain 'A' and (resid 175 through 274 )AA175 - 274174 - 273
33chain 'B' and (resid -1 through 11 )BB-1 - 111 - 13
44chain 'B' and (resid 12 through 41 )BB12 - 4114 - 43
55chain 'B' and (resid 42 through 61 )BB42 - 6144 - 63
66chain 'B' and (resid 62 through 99 )BB62 - 9964 - 101
77chain 'H' and (resid 2 through 39 )HC2 - 391 - 38
88chain 'H' and (resid 40 through 73 )HC40 - 7339 - 72
99chain 'H' and (resid 74 through 132 )HC74 - 13273 - 131
1010chain 'H' and (resid 133 through 201 )HC133 - 201132 - 200
1111chain 'H' and (resid 202 through 219 )HC202 - 219201 - 218
1212chain 'L' and (resid 1 through 102 )LD1 - 1021 - 102
1313chain 'L' and (resid 103 through 212 )LD103 - 212103 - 212
1414chain 'P' and (resid 1 through 10 )PE1 - 101 - 10

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