[English] 日本語
Yorodumi
- EMDB-65085: cryo-EM structure of alligator haemoglobin in the T-like conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65085
Titlecryo-EM structure of alligator haemoglobin in the T-like conformation
Map data
Sample
  • Complex: alligator haemoglobin in carboxy form
    • Protein or peptide: Hemoglobin subunit alpha
    • Protein or peptide: Hemoglobin subunit beta
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CARBON MONOXIDE
Keywordshaemoglobin / OXYGEN BINDING
Function / homology
Function and homology information


haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding ...haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesAlligator mississippiensis (American alligator)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsTakahashi K / Lee Y / Nishizawa T / Tame JRH
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Biorxiv / Year: 2025
Title: Conformational analysis of liganded human hemoglobin by cryo electron microscopy
Authors: Takahashi K / Lee Y / Nishizawa T / Tame JRH
History
DepositionJun 18, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_65085.png

Downloads & links

-
Map

FileDownload / File: emd_65085.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 256 pix.
= 261.12 Å		1.02 Å/pix.
x 256 pix.
= 261.12 Å		1.02 Å/pix.
x 256 pix.
= 261.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.1414192 - 3.3190079
Average (Standard dev.)-0.000005115495 (±0.056780048)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 261.12 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_65085_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_65085_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_65085_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : alligator haemoglobin in carboxy form

EntireName: alligator haemoglobin in carboxy form
Components
  • Complex: alligator haemoglobin in carboxy form
    • Protein or peptide: Hemoglobin subunit alpha
    • Protein or peptide: Hemoglobin subunit beta
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CARBON MONOXIDE

-
Supramolecule #1: alligator haemoglobin in carboxy form

SupramoleculeName: alligator haemoglobin in carboxy form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Alligator mississippiensis (American alligator)
Molecular weightTheoretical: 100 KDa

-
Macromolecule #1: Hemoglobin subunit alpha

MacromoleculeName: Hemoglobin subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Alligator mississippiensis (American alligator)
Molecular weightTheoretical: 15.891368 KDa
SequenceString:
MVLSMEDKSN VKAIWGKASG HLEEYGAEAL ERMFCAYPQT KIYFPHFDMS HNSAQIRAHG KKVFSALHEA VNHIDDLPGA LCRLSELHA HSLRVDPVNF KFLAHCVLVV FAIHHPSALS PEIHASLDKF LCAVSAVLTS KYR

UniProtKB: Hemoglobin subunit alpha

-
Macromolecule #2: Hemoglobin subunit beta

MacromoleculeName: Hemoglobin subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Alligator mississippiensis (American alligator)
Molecular weightTheoretical: 16.641213 KDa
SequenceString:
ASFDAHERKF IVDLWAKVDV AQCGADALSR MLIVYPWKRR YFEHFGKMCN AHDILHNSKV QEHGKKVLAS FGEAVKHLDN IKGHFANLS KLHCEKFHVD PENFKLLGDI IIIVLAAHHP EDFSVECHAA FQKLVRQVAA ALAAEYH

UniProtKB: Hemoglobin subunit beta

-
Macromolecule #3: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 3 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

-
Macromolecule #4: CARBON MONOXIDE

MacromoleculeName: CARBON MONOXIDE / type: ligand / ID: 4 / Number of copies: 2 / Formula: CMO
Molecular weightTheoretical: 28.01 Da
Chemical component information

ChemComp-CMO:
CARBON MONOXIDE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / 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 / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8wix

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 238763
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

8wix


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9vie:
cryo-EM structure of alligator haemoglobin in the T-like conformation

+
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