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- EMDB-54270: Cryo-EM structure of the LB_DQB0301_A Fab - HLA-DQB1*03:01/DQA1*0... -

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Basic information

Entry
Database: EMDB / ID: EMD-54270
TitleCryo-EM structure of the LB_DQB0301_A Fab - HLA-DQB1*03:01/DQA1*05:02 human alloantibody-HLA complex
Map data
Sample
  • Complex: LB_DQB0301_A - HLA-DQB1*03:01/DQA1*05:02
    • Protein or peptide: Peptide, unknown sequence.
    • Protein or peptide: LB_DQB0301_A Heavy chain
    • Protein or peptide: LB_DQB0301_A Light chain
    • Protein or peptide: HLA class II histocompatibility antigen, DQ beta 1 chain
    • Protein or peptide: HLA class II histocompatibility antigen, DQ alpha 1 chain
KeywordsHuman Leucocyte Antigens / Alloantibody / Antibody / Antigen / Epitope / protein-protein interaction / organ rejection / IMMUNE SYSTEM
Function / homology
Function and homology information


MHC class II receptor activity / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / humoral immune response / Generation of second messenger molecules / Co-inhibition by PD-1 / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane ...MHC class II receptor activity / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / humoral immune response / Generation of second messenger molecules / Co-inhibition by PD-1 / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / ER to Golgi transport vesicle membrane / clathrin-coated endocytic vesicle membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / positive regulation of T cell activation / Interferon gamma signaling / endocytic vesicle membrane / MHC class II protein complex binding / T cell receptor signaling pathway / late endosome membrane / Downstream TCR signaling / adaptive immune response / immune response / Golgi membrane / lysosomal membrane / membrane / plasma 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 1 chain / HLA class II histocompatibility antigen, DQ beta 1 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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_DQB0301_A Fab - HLA-DQB1*03:01/DQA1*05:02 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_54270.png

Downloads & links

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Map

FileDownload / File: emd_54270.map.gz / Format: CCP4 / Size: 476.8 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 500 pix.
= 255. Å		0.51 Å/pix.
x 500 pix.
= 255. Å		0.51 Å/pix.
x 500 pix.
= 255. 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: 0.045
Minimum - Maximum-0.1806206 - 0.25633347
Average (Standard dev.)-0.00015051257 (±0.0045859786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 255.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54270_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_54270_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 : LB_DQB0301_A - HLA-DQB1*03:01/DQA1*05:02

EntireName: LB_DQB0301_A - HLA-DQB1*03:01/DQA1*05:02
Components
  • Complex: LB_DQB0301_A - HLA-DQB1*03:01/DQA1*05:02
    • Protein or peptide: Peptide, unknown sequence.
    • Protein or peptide: LB_DQB0301_A Heavy chain
    • Protein or peptide: LB_DQB0301_A Light chain
    • Protein or peptide: HLA class II histocompatibility antigen, DQ beta 1 chain
    • Protein or peptide: HLA class II histocompatibility antigen, DQ alpha 1 chain

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Supramolecule #1: LB_DQB0301_A - HLA-DQB1*03:01/DQA1*05:02

SupramoleculeName: LB_DQB0301_A - HLA-DQB1*03:01/DQA1*05:02 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #5, #3-#4, #2, #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: HLA class II histocompatibility antigen, DQ alpha 1 chain

MacromoleculeName: HLA class II histocompatibility antigen, DQ alpha 1 chain
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.60102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EDIVADHVAS YGVNLYQSYG PSGQYTHEFD GDEQFYVDLG RKETVWCLPV LRQFRFDRQF ALTNIAVLKH NLNSLIKRSN STAATNEVP EVTVFSKSPV TLGQPNILIC LVDNIFPPVV NITWLSNGHS VTEGVSETSF LSKSDHSFFK ISYLTLLPSA E ESYDCKVE ...String:
EDIVADHVAS YGVNLYQSYG PSGQYTHEFD GDEQFYVDLG RKETVWCLPV LRQFRFDRQF ALTNIAVLKH NLNSLIKRSN STAATNEVP EVTVFSKSPV TLGQPNILIC LVDNIFPPVV NITWLSNGHS VTEGVSETSF LSKSDHSFFK ISYLTLLPSA E ESYDCKVE HWGLDKPLLK HWEPEIPAPM SELTETVVCA LGLSVGLVGI VVGTVFIIRG LRSVGASRHQ GPL

UniProtKB: HLA class II histocompatibility antigen, DQ alpha 1 chain

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Macromolecule #2: HLA class II histocompatibility antigen, DQ beta 1 chain

MacromoleculeName: HLA class II histocompatibility antigen, DQ beta 1 chain
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.671094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RDSPEDFVYQ FKAMCYFTNG TERVRYVTRY IYNREEYARF DSDVEVYRAV TPLGPPDAEY WNSQKEVLER TRAELDTVCR HNYQLELRT TLQRRVEPTV TISPSRTEAL NHHNLLVCSV TDFYPAQIKV RWFRNDQEET TGVVSTPLIR NGDWTFQILV M LEMTPQHG ...String:
RDSPEDFVYQ FKAMCYFTNG TERVRYVTRY IYNREEYARF DSDVEVYRAV TPLGPPDAEY WNSQKEVLER TRAELDTVCR HNYQLELRT TLQRRVEPTV TISPSRTEAL NHHNLLVCSV TDFYPAQIKV RWFRNDQEET TGVVSTPLIR NGDWTFQILV M LEMTPQHG DVYTCHVEHP SLQNPITVEW RAQSESAQSK MLSGIGGFVL GLIFLGLGLI IHHRSQKGLL H

UniProtKB: HLA class II histocompatibility antigen, DQ beta 1 chain

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Macromolecule #3: LB_DQB0301_A Heavy chain

MacromoleculeName: LB_DQB0301_A Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.442479 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EEQLVESGGG LVQAGGSLRL SCAASGFMFG SYWMTWVRQA PGKGLEWVAN IRQDGSAKYY VDSVRGRFTI SRDNAKNSLY LQMNSLRAE DTAVYYCGRV YSRGYSGYMW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String:
EEQLVESGGG LVQAGGSLRL SCAASGFMFG SYWMTWVRQA PGKGLEWVAN IRQDGSAKYY VDSVRGRFTI SRDNAKNSLY LQMNSLRAE DTAVYYCGRV YSRGYSGYMW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PKSCDKTHHH HHHHHHH

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Macromolecule #4: LB_DQB0301_A Light chain

MacromoleculeName: LB_DQB0301_A Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.573109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPAT LSLSPGERAT LSCRASQNVN NYLAWYQQKP GQAPRLLIYD ASNRATGVPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQ QRSDWPPGLT FGGGTKVEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
EIVLTQSPAT LSLSPGERAT LSCRASQNVN NYLAWYQQKP GQAPRLLIYD ASNRATGVPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQ QRSDWPPGLT FGGGTKVEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #5: Peptide, unknown sequence.

MacromoleculeName: Peptide, unknown sequence. / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 869.063 Da
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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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: Phosphate-buffered saline (PBS) 1x
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 202200
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9ruf:
Cryo-EM structure of the LB_DQB0301_A Fab - HLA-DQB1*03:01/DQA1*05:02 human alloantibody-HLA complex

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