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- PDB-7bbg: CRYSTAL STRUCTURE OF HLA-A2-WT1-RMF AND FAB 11D06 -

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Basic information

Entry
Database: PDB / ID: 7bbg
TitleCRYSTAL STRUCTURE OF HLA-A2-WT1-RMF AND FAB 11D06
Components
  • Beta-2-microglobulin
  • Heavy chain of Fab fragment 11D06
  • Light chain of Fab fragment 11D06
  • MHC class I antigen
  • Wilms tumor 1 (WT1) derived peptide
KeywordsIMMUNE SYSTEM / ANTIBODY / HLA / MHC / RMF PEPTIDE / WT1 / FAB FRAGMENT 11D06
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 / 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 / lumenal side of endoplasmic reticulum membrane ...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 / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / signaling receptor binding / 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 / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
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. ...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 / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsBujotzek, A. / Georges, G. / Hanisch, L.J. / Klein, C. / Benz, J.
CitationJournal: Blood / Year: 2021
Title: Targeting intracellular WT1 in AML with a novel RMF-peptide-MHC-specific T-cell bispecific antibody.
Authors: Augsberger, C. / Hanel, G. / Xu, W. / Pulko, V. / Hanisch, L.J. / Augustin, A. / Challier, J. / Hunt, K. / Vick, B. / Rovatti, P.E. / Krupka, C. / Rothe, M. / Schonle, A. / Sam, J. / Lezan, ...Authors: Augsberger, C. / Hanel, G. / Xu, W. / Pulko, V. / Hanisch, L.J. / Augustin, A. / Challier, J. / Hunt, K. / Vick, B. / Rovatti, P.E. / Krupka, C. / Rothe, M. / Schonle, A. / Sam, J. / Lezan, E. / Ducret, A. / Ortiz-Franyuti, D. / Walz, A.C. / Benz, J. / Bujotzek, A. / Lichtenegger, F.S. / Gassner, C. / Carpy, A. / Lyamichev, V. / Patel, J. / Konstandin, N. / Tunger, A. / Schmitz, M. / von Bergwelt-Baildon, M. / Spiekermann, K. / Vago, L. / Jeremias, I. / Marrer-Berger, E. / Umana, P. / Klein, C. / Subklewe, M.
History
DepositionDec 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 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 1.2May 1, 2024Group: 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: MHC class I antigen
B: Beta-2-microglobulin
C: Wilms tumor 1 (WT1) derived peptide
H: Heavy chain of Fab fragment 11D06
L: Light chain of Fab fragment 11D06
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,36610
Polymers95,2515
Non-polymers1155
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10510 Å2
ΔGint-104 kcal/mol
Surface area36480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.111, 67.009, 139.361
Angle α, β, γ (deg.)90.000, 90.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 35401.934 Da / Num. of mol.: 1
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: Q861F7
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
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, 1 molecules C

#3: Protein/peptide Wilms tumor 1 (WT1) derived peptide


Mass: 1109.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Antibody , 2 types, 2 molecules HL

#4: Antibody Heavy chain of Fab fragment 11D06


Mass: 23528.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#5: Antibody Light chain of Fab fragment 11D06


Mass: 23331.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 2 types, 255 molecules

#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.0, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.64→48.3 Å / Num. obs: 29643 / % possible obs: 99.8 % / Redundancy: 3.85 % / CC1/2: 0.992 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.1
Reflection shellResolution: 2.64→2.77 Å / Rmerge(I) obs: 0.97 / Num. unique obs: 3934 / CC1/2: 0.373

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house Fab fragment structure

Resolution: 2.64→48.3 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.658 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.668 / SU Rfree Blow DPI: 0.283 / SU Rfree Cruickshank DPI: 0.287
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1425 4.81 %RANDOM
Rwork0.168 ---
obs0.171 29606 99.9 %-
Displacement parametersBiso max: 167.6 Å2 / Biso mean: 67.15 Å2 / Biso min: 26.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.0654 Å20 Å211.1887 Å2
2---0.7973 Å20 Å2
3---0.7319 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 2.64→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6387 0 5 250 6642
Biso mean--67.94 57.47 -
Num. residues----810
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2207SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes151HARMONIC2
X-RAY DIFFRACTIONt_gen_planes957HARMONIC5
X-RAY DIFFRACTIONt_it6569HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion843SEMIHARMONIC5
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_contact6900SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6569HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8928HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion20.45
LS refinement shellResolution: 2.64→2.73 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.27 153 5.27 %
Rwork0.224 2751 -
all0.227 2904 -
obs--99.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.76040.0057-0.00360.92640.45522.30880.0152-0.06470.1630.2174-0.0457-0.0933-0.0285-0.1490.0305-0.1108-0.0429-0.0934-0.1619-0.0094-0.17063.328434.1363-31.6228
21.0257-0.2452-1.01413.6034-2.73015.46990.0588-0.3812-0.10250.334-0.027-0.02060.59150.2075-0.0318-0.0114-0.0872-0.08450.02350.1083-0.20958.977421.9741-17.8914
31.27890.0917-0.5910.65730.11321.92740.11290.242-0.081-0.2242-0.09010.0763-0.0289-0.2547-0.0227-0.01120.0752-0.1064-0.1713-0.0183-0.07517.186130.7606-87.2762
41.06120.1262-0.75580.461-0.38942.19610.05650.02770.0964-0.1707-0.1102-0.1378-0.07390.1630.0536-0.0510.06980.006-0.17960.0021-0.035924.412233.7795-85.7375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 274
2X-RAY DIFFRACTION2{ B|* }B1 - 100
3X-RAY DIFFRACTION3{ H|* }H2 - 223
4X-RAY DIFFRACTION4{ L|* }L1 - 212

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