[English] 日本語
Yorodumi
- EMDB-43047: Structure of human AQP4 with a pathogenic autoantibody- rAB 58 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43047
TitleStructure of human AQP4 with a pathogenic autoantibody- rAB 58
Map dataSharpened map
Sample
  • Complex: Human AQP4 tetramer bound to Fab fragment of the pathogenic autoantibody- rAB 58
    • Protein or peptide: Aquaporin-4
    • Protein or peptide: rAB 58 Light Chain
    • Protein or peptide: rAB 58 Heavy Chain
  • Ligand: water
KeywordsAquaporin / Water-channel / TRANSPORT PROTEIN-IMMUNE SYSTEM complex / Neuromyelitis Optica (NMO) / Autoimmune disease
Function / homology
Function and homology information


Passive transport by Aquaporins / cerebrospinal fluid circulation / astrocyte end-foot / intracellular water homeostasis / water transport / water channel activity / multicellular organismal-level water homeostasis / renal water homeostasis / sarcolemma / cellular response to type II interferon ...Passive transport by Aquaporins / cerebrospinal fluid circulation / astrocyte end-foot / intracellular water homeostasis / water transport / water channel activity / multicellular organismal-level water homeostasis / renal water homeostasis / sarcolemma / cellular response to type II interferon / Vasopressin regulates renal water homeostasis via Aquaporins / basolateral plasma membrane / protein homotetramerization / endosome membrane / external side of plasma membrane / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGupta M / Khandelwal NK / Stroud RM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Human AQP4 structure in lipid nanodisc using cryo-EM
Authors: Gupta M / Khandelwal NK / Stroud RM
History
DepositionDec 7, 2023-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43047.png

Downloads & links

-
Map

FileDownload / File: emd_43047.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 392 pix.
= 326.928 Å		0.83 Å/pix.
x 392 pix.
= 326.928 Å		0.83 Å/pix.
x 392 pix.
= 326.928 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-1.5190842 - 2.8478935
Average (Standard dev.)0.0013576356 (±0.051415592)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 326.928 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map

Fileemd_43047_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43047_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_43047_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human AQP4 tetramer bound to Fab fragment of the pathogenic autoa...

EntireName: Human AQP4 tetramer bound to Fab fragment of the pathogenic autoantibody- rAB 58
Components
  • Complex: Human AQP4 tetramer bound to Fab fragment of the pathogenic autoantibody- rAB 58
    • Protein or peptide: Aquaporin-4
    • Protein or peptide: rAB 58 Light Chain
    • Protein or peptide: rAB 58 Heavy Chain
  • Ligand: water

-
Supramolecule #1: Human AQP4 tetramer bound to Fab fragment of the pathogenic autoa...

SupramoleculeName: Human AQP4 tetramer bound to Fab fragment of the pathogenic autoantibody- rAB 58
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Aquaporin-4

MacromoleculeName: Aquaporin-4 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.862586 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MSDRPTARRW GKCGPLCTRE NIMVAFKGVW TQAFWKAVTA EFLAMLIFVL LSLGSTINWG GTEKPLPVDM VLISLCFGLS IATMVQCFG HISGGHINPA VTVAMVCTRK ISIAKSVFYI AAQCLGAIIG AGILYLVTPP SVVGGLGVTM VHGNLTAGHG L LVELIITF ...String:
MSDRPTARRW GKCGPLCTRE NIMVAFKGVW TQAFWKAVTA EFLAMLIFVL LSLGSTINWG GTEKPLPVDM VLISLCFGLS IATMVQCFG HISGGHINPA VTVAMVCTRK ISIAKSVFYI AAQCLGAIIG AGILYLVTPP SVVGGLGVTM VHGNLTAGHG L LVELIITF QLVFTIFASC DSKRTDVTGS IALAIGFSVA IGHLFAINYT GASMNPARSF GPAVIMGNWE NHWIYWVGPI IG AVLAGGL YEYVFCPDVE FKRRFKEAFS KAAQQTKGSY MEVEDNRSQV ETDDLILKPG VVHVIDVDRG EEKKGKDQSG EVL SSV

UniProtKB: Aquaporin-4

-
Macromolecule #2: rAB 58 Light Chain

MacromoleculeName: rAB 58 Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.497053 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSA LSASVGDTVT ITCRASQSIR SWLAWYQQKP GKAPKLLIYK ASDLQSGVPS RFSGSGSGTD FTLTISGLQP DDFATYYCQ HYNSYPYTFG QGTKVEIRRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSA LSASVGDTVT ITCRASQSIR SWLAWYQQKP GKAPKLLIYK ASDLQSGVPS RFSGSGSGTD FTLTISGLQP DDFATYYCQ HYNSYPYTFG QGTKVEIRRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

-
Macromolecule #3: rAB 58 Heavy Chain

MacromoleculeName: rAB 58 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.423158 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGGG LVQPGGSLRL SCAASGFTFR GYAMNWVRQA PGKGLEWVAS ISGSGSITQY ADSAKGRFTI TRDNSKSTLY AHVSSLRAD DTAVYYCAKG DYVFDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT ...String:
QVQLVESGGG LVQPGGSLRL SCAASGFTFR GYAMNWVRQA PGKGLEWVAS ISGSGSITQY ADSAKGRFTI TRDNSKSTLY AHVSSLRAD DTAVYYCAKG DYVFDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS CDKTH

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 87 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: OTHER / Average electron dose: 60.0 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

+
Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3gd8

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 323342
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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