[English] 日本語
Yorodumi
- EMDB-73037: Transferrin Binding Protein A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-73037
TitleTransferrin Binding Protein A
Map data
Sample
  • Complex: Transferrin binding protein A
    • Protein or peptide: Transferrin-binding protein A
KeywordsMembrane protein / metal transporter / iron import / ton B-dependent transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


ferric iron transmembrane transporter activity / siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / cell outer membrane
Similarity search - Function
TonB-dependent lactoferrin/transferrin receptor / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / TonB-dependent receptor (TBDR) proteins signature 1. / TonB box, conserved site / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like ...TonB-dependent lactoferrin/transferrin receptor / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / TonB-dependent receptor (TBDR) proteins signature 1. / TonB box, conserved site / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily
Similarity search - Domain/homology
Transferrin-binding protein A
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsDubey S / Noinaj N
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI127793 United States
CitationJournal: To Be Published
Title: Transferrin Binding Protein A in complex with transferrin (iron bound in N lobe only)
Authors: Dubey S / Noinaj N
History
DepositionOct 5, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_73037.png

Downloads & links

-
Map

FileDownload / File: emd_73037.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: 0.186
Minimum - Maximum-0.27958536 - 0.53178
Average (Standard dev.)0.00062177295 (±0.019298397)
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

-
Half map: #1

Fileemd_73037_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_73037_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Transferrin binding protein A

EntireName: Transferrin binding protein A
Components
  • Complex: Transferrin binding protein A
    • Protein or peptide: Transferrin-binding protein A

-
Supramolecule #1: Transferrin binding protein A

SupramoleculeName: Transferrin binding protein A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria)
Molecular weightTheoretical: 100 KDa

-
Macromolecule #1: Transferrin-binding protein A

MacromoleculeName: Transferrin-binding protein A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria)
Molecular weightTheoretical: 102.506891 KDa
Recombinant expressionOrganism: Escherichia coli 0.1197 (bacteria)
SequenceString: MSNHHHHHHH HHHENLYFQG AMDIENVQAG QAQEKQLDTI QVKAKKQKTR RDNEVTGLGK LVKSSDTLSK EQVLNIRDLT RYDPGIAVV EQGRGASSGY SIRGMDKNRV SLTVDGVSQI QSYTAQAALG GTRTAGSSGA INEIEYENVK AVEISKGSNS V EQGSGALA ...String:
MSNHHHHHHH HHHENLYFQG AMDIENVQAG QAQEKQLDTI QVKAKKQKTR RDNEVTGLGK LVKSSDTLSK EQVLNIRDLT RYDPGIAVV EQGRGASSGY SIRGMDKNRV SLTVDGVSQI QSYTAQAALG GTRTAGSSGA INEIEYENVK AVEISKGSNS V EQGSGALA GSVAFQTKTA DDVIGEGRQW GIQSKTAYSG KNRGLTQSIA LAGRIGGAEA LLIHTGRRAG EIRAHEDAGR GV QSFNRLV PVEDSSNYAY FIVKEECKNG SYETCKANPK KDVVGKDERQ TVSTRDYTGP NRFLADPLSY ESRSWLFRPG FRF ENKRHY IGGILEHTQQ TFDTRDMTVP AFLTKAVFDA NKKQAGSLPG NGKYAGNHKY GGLFTNGENG ALVGAEYGTG VFYD ETHTK SRYGLEYVYT NADKDTWADY ARLSYDRQGV GLDNHFQQTH CSADGSDKYC RPSADKPFSY YKSDRVIYGE SHRLL QAAF KKSFDAAKIR HNLSMNLGFD RFGSNMRHQD YYYQHANRAY SSNTPPQNNG KKISPNGSET SPYWVTIGRG NVVTGQ ICR LGNNTYTDCT PRSINGKSYY AAVRDNVRLG RWADVGAGLR YDYRSTHSDD GSVSTGTHRT LSWNAGIVLK PTDWLDL TY RTSTGFRLPS FAEMYGWRAG VQSKAVKIDP EKSFNKEAGI VFKGDFGNLE ASWFNNAYRD LIVRGYEAQI KDGKEEAK G DPAYLNAQSA RITGINILGK IDWNGVWDKL PEGWYSTFAY NRMRVRDIKK RADRTDIQSH LFDAIQPSRY VVGLGYDQP EGKWGVNGML TYSKAKEITE LLGSRALLNG NSRNTKATAR RTRPWYIVDV SGYYTVKKHF TLRAGVYNLM NYRYVTWENV RQTAGGAVN QHKNVGVYNR YAAPGRNYTF SLEMKF

UniProtKB: Transferrin-binding protein A

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.0 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: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3v89

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 66000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9yjw:
Transferrin Binding Protein A

+
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