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- EMDB-54272: Cryo-EM structure of the LB_DQB0602_B Fab - HLA-DQB1*06:02/DQA1*0... -

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Basic information

Entry
Database: EMDB / ID: EMD-54272
TitleCryo-EM structure of the LB_DQB0602_B Fab - HLA-DQB1*06:02/DQA1*01:02 human alloantibody-HLA complex
Map data
Sample
  • Complex: Fab LB_DQB0602_B - HLA-DQB1*06:02/DQA1*01:02
    • Protein or peptide: Peptide, unknown sequence
    • Protein or peptide: LB_DQB0602_B Heavy chain
    • Protein or peptide: LB_DQB0602_B Light chain
    • Protein or peptide: HLA class II histocompatibility antigen DQ beta chain
    • Protein or peptide: HLA class II histocompatibility antigen DQ alpha chain
KeywordsHuman Leucocyte Antigens / Alloantibody / Antibody / Antigen / Epitope / protein-protein interaction / organ rejection / IMMUNE SYSTEM
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / endosome membrane / lysosomal membrane
Similarity search - Function
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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
HLA class II histocompatibility antigen DQ alpha chain / HLA class II histocompatibility antigen DQ beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsZampieri V / Priddey A / Kosmoliaptsis V / Marquez JA
Funding supportEuropean Union, United Kingdom, United States, 5 items
OrganizationGrant numberCountry
European Union (EU)101094131European Union
European Union (EU)847543European Union
National Institute for Health and Care ResearchPDF-2016-09-065 United Kingdom
Terasaki InstituteG106170 United States
NIHR Blood and Transplant Research Unit in Organ Donation and TransplantationNIHR203332 United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of the LB_DQB0602_B Fab - HLA-DQB1*06:02/DQA1*01:02 human alloantibody-HLA complex
Authors: Zampieri V / Priddey A / Kosmoliaptsis V / Marquez JA
History
DepositionJul 4, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54272.png

Downloads & links

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Map

FileDownload / File: emd_54272.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.51 Å/pix.
x 400 pix.
= 204. Å		0.51 Å/pix.
x 400 pix.
= 204. Å		0.51 Å/pix.
x 400 pix.
= 204. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.51 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.088680826 - 0.20602918
Average (Standard dev.)0.00004552363 (±0.0053035063)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 204.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54272_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54272_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Fab LB_DQB0602_B - HLA-DQB1*06:02/DQA1*01:02

EntireName: Fab LB_DQB0602_B - HLA-DQB1*06:02/DQA1*01:02
Components
  • Complex: Fab LB_DQB0602_B - HLA-DQB1*06:02/DQA1*01:02
    • Protein or peptide: Peptide, unknown sequence
    • Protein or peptide: LB_DQB0602_B Heavy chain
    • Protein or peptide: LB_DQB0602_B Light chain
    • Protein or peptide: HLA class II histocompatibility antigen DQ beta chain
    • Protein or peptide: HLA class II histocompatibility antigen DQ alpha chain

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Supramolecule #1: Fab LB_DQB0602_B - HLA-DQB1*06:02/DQA1*01:02

SupramoleculeName: Fab LB_DQB0602_B - HLA-DQB1*06:02/DQA1*01:02 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Peptide, unknown sequence

MacromoleculeName: Peptide, unknown sequence / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.039273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #2: LB_DQB0602_B Heavy chain

MacromoleculeName: LB_DQB0602_B Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.326412 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVHLVESGGG VVQPGRSLRL SCAASGFSFS NYAMHWVRQA PGTGLEWVAV IWYDGGNKYY ADSVKGRFTI SRDTSKNTLY LQMNSLRAE DTAVYYCARE PEPTLTTLHY YYAMDVWGQG TTVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
QVHLVESGGG VVQPGRSLRL SCAASGFSFS NYAMHWVRQA PGTGLEWVAV IWYDGGNKYY ADSVKGRFTI SRDTSKNTLY LQMNSLRAE DTAVYYCARE PEPTLTTLHY YYAMDVWGQG TTVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS CDKTHHHHHH HH HH

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Macromolecule #3: LB_DQB0602_B Light chain

MacromoleculeName: LB_DQB0602_B Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.592217 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGERAT LSCRASQSVP SSYLAWYQQK PGQAPRLLIY GATNRATGIS DRFSGGGSGT DFTLTISRLE PEDFAVYYC QQFATSPMYT FGQGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
EIVLTQSPGT LSLSPGERAT LSCRASQSVP SSYLAWYQQK PGQAPRLLIY GATNRATGIS DRFSGGGSGT DFTLTISRLE PEDFAVYYC QQFATSPMYT FGQGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #4: HLA class II histocompatibility antigen DQ beta chain

MacromoleculeName: HLA class II histocompatibility antigen DQ beta chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.367811 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RDSPEDFVFQ FKGMCYFTNG TERVRLVTRY IYNREEYARF DSDVGVYRAV TPQGRPDAEY WNSQKEVLEG TRAELDTVCR HNYEVAFRG ILQRRVEPTV TISPSRTEAL NHHNLLVCSV TDFYPGQIKV RWFRNDQEET AGVVSTPLIR NGDWTFQILV M LEMTPQRG ...String:
RDSPEDFVFQ FKGMCYFTNG TERVRLVTRY IYNREEYARF DSDVGVYRAV TPQGRPDAEY WNSQKEVLEG TRAELDTVCR HNYEVAFRG ILQRRVEPTV TISPSRTEAL NHHNLLVCSV TDFYPGQIKV RWFRNDQEET AGVVSTPLIR NGDWTFQILV M LEMTPQRG DVYTCHVEHP SLQSPITVEW RAQSESAQSK MLSGVGGFVL GLIFLGLGLI IRQRSQKGLL H

UniProtKB: HLA class II histocompatibility antigen DQ beta chain

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Macromolecule #5: HLA class II histocompatibility antigen DQ alpha chain

MacromoleculeName: HLA class II histocompatibility antigen DQ alpha chain
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.752049 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EDIVADHVAS CGVNLYQFYG PSGQYTHEFD GDEQFYVDLE RKETAWRWPE FSKFGGFDPQ GALRNMAVAK HNLNIMIKRY NSTAATNEV PEVTVFSKSP VTLGQPNTLI CLVDNIFPPV VNITWLSNGQ SVTEGVSETS FLSKSDHSFF KISYLTFLPS A DEIYDCKV ...String:
EDIVADHVAS CGVNLYQFYG PSGQYTHEFD GDEQFYVDLE RKETAWRWPE FSKFGGFDPQ GALRNMAVAK HNLNIMIKRY NSTAATNEV PEVTVFSKSP VTLGQPNTLI CLVDNIFPPV VNITWLSNGQ SVTEGVSETS FLSKSDHSFF KISYLTFLPS A DEIYDCKV EHWGLDQPLL KHWEPEIPAP MSELTETVVC ALGLSVGLMG IVVGTVFIIQ GLRSVGASRH QGPL

UniProtKB: HLA class II histocompatibility antigen DQ alpha chain

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: PBS x1
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 12686 / Average electron dose: 49.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 278615
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9ruh:
Cryo-EM structure of the LB_DQB0602_B Fab - HLA-DQB1*06:02/DQA1*01:02 human alloantibody-HLA complex

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