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- PDB-6id4: Defining the structural basis for human alloantibody binding to h... -

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Basic information

Entry
Database: PDB / ID: 6id4
TitleDefining the structural basis for human alloantibody binding to human leukocyte antigen allele HLA-A*11:01
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Heavy chain
  • Light chain
  • MHC class I antigen
  • peptide
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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. ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLescar, J. / Wong, Y.H. / Liew, C.W. / Gu, Y. / MacAry, P.A.
CitationJournal: Nat Commun / Year: 2019
Title: Defining the structural basis for human alloantibody binding to human leukocyte antigen allele HLA-A*11:01.
Authors: Gu, Y. / Wong, Y.H. / Liew, C.W. / Chan, C.E.Z. / Murali, T.M. / Yap, J. / Too, C.T. / Purushotorman, K. / Hamidinia, M. / El Sahili, A. / Goh, A.T.H. / Teo, R.Z.C. / Wood, K.J. / Hanson, B. ...Authors: Gu, Y. / Wong, Y.H. / Liew, C.W. / Chan, C.E.Z. / Murali, T.M. / Yap, J. / Too, C.T. / Purushotorman, K. / Hamidinia, M. / El Sahili, A. / Goh, A.T.H. / Teo, R.Z.C. / Wood, K.J. / Hanson, B.J. / Gascoigne, N.R.J. / Lescar, J. / Vathsala, A. / MacAry, P.A.
History
DepositionSep 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 2.0Oct 28, 2020Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Polymer sequence / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_instance_feature / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.formula_weight / _entity.pdbx_description ..._entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 2.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Heavy chain
D: Light chain
E: MHC class I antigen
F: Beta-2-microglobulin
H: Heavy chain
L: Light chain
T: peptide
U: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,29220
Polymers184,30110
Non-polymers99110
Water14,466803
1
A: MHC class I antigen
B: Beta-2-microglobulin
H: Heavy chain
L: Light chain
U: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,63910
Polymers92,1515
Non-polymers4895
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10840 Å2
ΔGint-33 kcal/mol
Surface area36190 Å2
MethodPISA
2
C: Heavy chain
D: Light chain
E: MHC class I antigen
F: Beta-2-microglobulin
T: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,65310
Polymers92,1515
Non-polymers5035
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11030 Å2
ΔGint-31 kcal/mol
Surface area36290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.560, 215.330, 80.980
Angle α, β, γ (deg.)90.00, 92.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules AEBF

#1: Protein MHC class I antigen


Mass: 31986.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: F6IQY1
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules TU

#5: Protein/peptide peptide /


Mass: 1013.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1

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Antibody , 2 types, 4 molecules CHDL

#3: Antibody Heavy chain


Mass: 23629.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Antibody Light chain /


Mass: 23642.318 Da / Num. of mol.: 2
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, 813 molecules

#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 803 / Source method: isolated from a natural source / Formula: H2O

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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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1,4-Dioxane, Tris pH 8.2, Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.39→48.69 Å / Num. obs: 79954 / % possible obs: 96.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 68.79 Å2 / CC1/2: 0.98 / Net I/σ(I): 6.2
Reflection shellResolution: 2.39→2.41 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.36 / Num. unique obs: 12545 / CC1/2: 0.56 / % possible all: 93.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
PHENIXphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W72

1w72


Resolution: 2.4→45.78 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.352 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.353 / SU Rfree Blow DPI: 0.244 / SU Rfree Cruickshank DPI: 0.247
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3997 5 %RANDOM
Rwork0.197 ---
obs0.199 79940 96.5 %-
Displacement parametersBiso mean: 61.53 Å2
Baniso -1Baniso -2Baniso -3
1--3.3015 Å20 Å2-2.9029 Å2
2--3.9228 Å20 Å2
3----0.6213 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.4→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12761 0 65 808 13634
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113220HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2317980HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4422SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes309HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1917HARMONIC5
X-RAY DIFFRACTIONt_it13220HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion20.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1679SEMIHARMONIC5
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_contact14328SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2659 287 5 %
Rwork0.2387 5453 -
all0.24 5740 -
obs--93.84 %
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)
10.9015-0.0745-0.25231.02190.19630.9525-0.0083-0.06950.1201-0.0732-0.00980.1167-0.1846-0.20990.0181-0.13740.0218-0.0937-0.0335-0.0001-0.1279-15.6692-4.123416.6226
22.32430.0011-0.40252.84510.63531.00670.04420.02570.65570.02770.0756-0.229-0.3530.0459-0.1198-0.05860.008-0.0812-0.15190.01640.0481-2.30459.541915.8883
33.2066-0.4122-0.60780.17450.2551-0.0714-0.05630.1068-0.038-0.02040.0503-0.12450.0214-0.14940.006-0.08320.0449-0.00260.00850.042-0.0416-19.728750.7915-28.6469
43.36780.1685-0.27740.16710.3653-0.0377-0.0782-0.63960.2786-0.25550.1133-0.1416-0.14470.0578-0.0351-0.07590.0351-0.01250.08620.0113-0.1129-15.740557.7912-11.3726
50.99080.0950.38610.87460.17980.98720.0788-0.0909-0.0750.1175-0.00220.16810.2724-0.402-0.0766-0.1402-0.05890.00810.04850.0208-0.1679-73.916150.1263-17.119
61.9354-0.53560.36794.4240.31511.33520.0692-0.0714-0.4767-0.10370.035-0.32550.48250.1036-0.1043-0.0602-0.01160.0031-0.1510.06270.0152-60.107937.1445-16.158
72.69710.41690.5080.57940.17460.04530.0771-0.1882-0.05410.0136-0.021-0.222-0.0172-0.1841-0.0561-0.0992-0.0408-0.05480.05020.0217-0.088338.3208-3.980328.8031
82.8118-0.44590.89070.57890.4040.10490.07270.3681-0.12320.27760.0621-0.21960.17260.1584-0.1348-0.0935-0.0155-0.13570.11160.0166-0.104442.5738-10.704211.5366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ H|* }
8X-RAY DIFFRACTION8{ L|* }

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