[English] 日本語
Yorodumi
- EMDB-54271: Cryo-EM structure of the LB_DQB0303_A Fab - HLA-DQB1*03:03/DQA1*0... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54271
TitleCryo-EM structure of the LB_DQB0303_A Fab - HLA-DQB1*03:03/DQA1*02:01 human alloantibody-HLA complex
Map data
Sample
  • Complex: LB_DQB0303_A - HLADQB1*03:03/DQA1*02:01
    • Protein or peptide: LB_DQB0303_A Heavy chain
    • Protein or peptide: LB_DQB0303_A Light chain
    • Protein or peptide: Lymphocyte antigen
    • Protein or peptide: HLA class II histocompatibility antigen DQ alpha chain
    • Protein or peptide: Peptide, unknown sequence
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 / Lymphocyte antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsZampieri V / Priddey A / Linares R / 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_DQB0303_A Fab - HLA-DQB1*03:03/DQA1*02:01 human alloantibody-HLA complex
Authors: Zampieri V / Priddey A / Linares R / 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

-
Structure visualization

Supplemental images

emd_54271.png

Downloads & links

-
Map

FileDownload / File: emd_54271.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: 0.035
Minimum - Maximum-0.109062955 - 0.20216186
Average (Standard dev.)-0.00016193409 (±0.005108269)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #2

Fileemd_54271_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_54271_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : LB_DQB0303_A - HLADQB1*03:03/DQA1*02:01

EntireName: LB_DQB0303_A - HLADQB1*03:03/DQA1*02:01
Components
  • Complex: LB_DQB0303_A - HLADQB1*03:03/DQA1*02:01
    • Protein or peptide: LB_DQB0303_A Heavy chain
    • Protein or peptide: LB_DQB0303_A Light chain
    • Protein or peptide: Lymphocyte antigen
    • Protein or peptide: HLA class II histocompatibility antigen DQ alpha chain
    • Protein or peptide: Peptide, unknown sequence

-
Supramolecule #1: LB_DQB0303_A - HLADQB1*03:03/DQA1*02:01

SupramoleculeName: LB_DQB0303_A - HLADQB1*03:03/DQA1*02:01 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: LB_DQB0303_A Heavy chain

MacromoleculeName: LB_DQB0303_A Heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.521527 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGFTLS TYEMNWVRQA PGKGLEWVSY SSRSGGNRFY ADSVKGRFTI SRDNAKNSLF LQMNSLRVE DTAVYYCARD HAHIEATGPL DCWGLGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
EVQLVESGGG LVQPGGSLRL SCAASGFTLS TYEMNWVRQA PGKGLEWVSY SSRSGGNRFY ADSVKGRFTI SRDNAKNSLF LQMNSLRVE DTAVYYCARD HAHIEATGPL DCWGLGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT HHHHHHHHHH

-
Macromolecule #2: LB_DQB0303_A Light chain

MacromoleculeName: LB_DQB0303_A Light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.521066 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPST LSASVGDRVT ITCRASQSIS SWLAWYQQKP GKAPKILIYD ASSLETGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYFSYPGFTF GPGTKVDIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPST LSASVGDRVT ITCRASQSIS SWLAWYQQKP GKAPKILIYD ASSLETGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYFSYPGFTF GPGTKVDIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

-
Macromolecule #3: Lymphocyte antigen

MacromoleculeName: Lymphocyte antigen / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.791457 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
RDSPEDFVYQ FKGMCYFTNG TERVRLVTRY IYNREEYARF DSDVGVYRAV TPLGPPDAEY WNSQKEVLER TRAELDTVCR HNYQLELRT TLQRRVEPTV TISPSRTEAL NHHNLLVCSV TDFYPAQIKV RWFRNDQEET TGVVSTPLIR NGDWTFQILV M LEMTPQRG DVYTCHVEHP SLQNPII

UniProtKB: Lymphocyte antigen

-
Macromolecule #4: HLA class II histocompatibility antigen DQ alpha chain

MacromoleculeName: HLA class II histocompatibility antigen DQ alpha chain
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.463811 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EDIVADHVAS YGVNLYQSYG PSGQFTHEFD GDEEFYVDLE RKETVWKLPL FHRLRFDPQF ALTNIAVLKH NLNILIKRSN STAATNEVP EVTVFSKSPV TLGQPNTLIC LVDNIFPPVV NITWLSNGHS VTEGVSETSF LSKSDHSFFK ISYLTFLPSA D EIYDCKVE ...String:
EDIVADHVAS YGVNLYQSYG PSGQFTHEFD GDEEFYVDLE RKETVWKLPL FHRLRFDPQF ALTNIAVLKH NLNILIKRSN STAATNEVP EVTVFSKSPV TLGQPNTLIC LVDNIFPPVV NITWLSNGHS VTEGVSETSF LSKSDHSFFK ISYLTFLPSA D EIYDCKVE HWGLDEPLLK HWEPEIPAPM SELTETVVCA LGLSVGLVGI VVGTVLIIRG LRSVGASRHQ G

UniProtKB: HLA class II histocompatibility antigen DQ alpha chain

-
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: 1.039273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Details: PBS x1
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.65 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
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: 739468
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

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

PDB-9rug:
Cryo-EM structure of the LB_DQB0303_A Fab - HLA-DQB1*03:03/DQA1*02:01 human alloantibody-HLA complex

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more