[English] 日本語
Yorodumi
- EMDB-73667: Neisseria gonorrhoeae Transferrin Binding Protein A in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-73667
TitleNeisseria gonorrhoeae Transferrin Binding Protein A in complex with Transferrin Binding Protein B and transferrin (iron bound in N lobe only)
Map data
Sample
  • Complex: Transferrin binding protein A/ B/Tf
    • Complex: NgTbpA
      • Protein or peptide: Transferrin-binding protein A
    • Complex: Tf
      • Protein or peptide: Transferrin
    • Complex: NmTbpB
      • Protein or peptide: Transferrin-binding protein B
  • Ligand: BICARBONATE ION
  • Ligand: FE (III) ION
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 / iron chaperone activity / siderophore uptake transmembrane transporter activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding ...ferric iron transmembrane transporter activity / siderophore transmembrane transport / iron chaperone activity / siderophore uptake transmembrane transporter activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding / osteoclast differentiation / basal plasma membrane / Post-translational protein phosphorylation / cell outer membrane / iron ion transport / clathrin-coated endocytic vesicle membrane / regulation of protein stability / HFE-transferrin receptor complex / cellular response to iron ion / Iron uptake and transport / ferrous iron binding / positive regulation of receptor-mediated endocytosis / recycling endosome / multicellular organismal-level iron ion homeostasis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / late endosome / Platelet degranulation / Cargo recognition for clathrin-mediated endocytosis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Clathrin-mediated endocytosis / antibacterial humoral response / cytoplasmic vesicle / secretory granule lumen / blood microparticle / vesicle / intracellular iron ion homeostasis / transmembrane transporter binding / early endosome / cell surface receptor signaling pathway / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / perinuclear region of cytoplasm / enzyme binding / cell surface / : / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
TonB-dependent lactoferrin/transferrin receptor / Transferrin-binding protein B, N-lobe handle / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / N-Lobe handle Tf-binding protein B / Transferrin-binding protein B, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / TbpB, N-lobe handle domain superfamily / Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B ...TonB-dependent lactoferrin/transferrin receptor / Transferrin-binding protein B, N-lobe handle / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / N-Lobe handle Tf-binding protein B / Transferrin-binding protein B, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / TbpB, N-lobe handle domain superfamily / Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / TonB-dependent receptor (TBDR) proteins signature 1. / Serotransferrin, mammalian / 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 / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin / Outer membrane protein/outer membrane enzyme PagP, beta-barrel
Similarity search - Domain/homology
Serotransferrin / Transferrin-binding protein A / Transferrin-binding protein B
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria) / Neisseria gonorrhoeae (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.26 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: Neisseria gonorrhoeae Transferrin Binding Protein A in complex with Transferrin Binding Protein B and transferrin (iron bound in N lobe only)
Authors: Dubey S / Noinaj N
History
DepositionOct 29, 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_73667.png

Downloads & links

-
Map

FileDownload / File: emd_73667.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.)
1.08 Å/pix.
x 256 pix.
= 275.968 Å		1.08 Å/pix.
x 256 pix.
= 275.968 Å		1.08 Å/pix.
x 256 pix.
= 275.968 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.078 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.2302398 - 0.45670745
Average (Standard dev.)0.0037864572 (±0.021997511)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 275.968 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_73667_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_73667_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Transferrin binding protein A/ B/Tf

EntireName: Transferrin binding protein A/ B/Tf
Components
  • Complex: Transferrin binding protein A/ B/Tf
    • Complex: NgTbpA
      • Protein or peptide: Transferrin-binding protein A
    • Complex: Tf
      • Protein or peptide: Transferrin
    • Complex: NmTbpB
      • Protein or peptide: Transferrin-binding protein B
  • Ligand: BICARBONATE ION
  • Ligand: FE (III) ION

-
Supramolecule #1: Transferrin binding protein A/ B/Tf

SupramoleculeName: Transferrin binding protein A/ B/Tf / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3, #1-#2
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria)
Molecular weightTheoretical: 88 KDa

-
Supramolecule #2: NgTbpA

SupramoleculeName: NgTbpA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Neisseria gonorrhoeae (bacteria)

-
Supramolecule #3: Tf

SupramoleculeName: Tf / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #4: NmTbpB

SupramoleculeName: NmTbpB / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria)

-
Macromolecule #1: Transferrin

MacromoleculeName: Transferrin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.153906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRLAVGALLV CAVLGLCLAV PDKTVRWCAV SEHEATKCQS FRDHMKSVIP SDGPSVACVK KASYLDCIRA IAANEADAVT LDAGLVYDA YLAPNNLKPV VAEFYGSKED PQTFYYAVAV VKKDSGFQMN QLRGKKSCHT GLGRSAGWNI PIGLLYCDLP E PRKPLEKA ...String:
MRLAVGALLV CAVLGLCLAV PDKTVRWCAV SEHEATKCQS FRDHMKSVIP SDGPSVACVK KASYLDCIRA IAANEADAVT LDAGLVYDA YLAPNNLKPV VAEFYGSKED PQTFYYAVAV VKKDSGFQMN QLRGKKSCHT GLGRSAGWNI PIGLLYCDLP E PRKPLEKA VANFFSGSCA PCADGTDFPQ LCQLCPGCGC STLNQYFGYS GAFKCLKDGA GDVAFVKHST IFENLANKAD RD QYELLCL DNTRKPVDEY KDCHLAQVPS HTVVARSMGG KEDLIWELLN QAQEHFGKDK SKEFQLFSSP HGKDLLFKDS AHG FLKVPP RMDAKMYLGY EYVTAIRNLR EGTCPEAPTD ECKPVKWCAL SHHERLKCDE WSVNSVGKIE CVSAETTEDC IAKI MNGEA DAMSLDGGFV YIAGKCGLVP VLAENYNKSD NCEDTPEAGY FAVAVVKKSA SDLTWDNLKG KKSCHTAVGR TAGWN IPMG LLYNKINHCR FDEFFSEGCA PGSKKDSSLC KLCMGSGLNL CEPNNKEGYY GYTGAFRCLV EKGDVAFVKH QTVPQN TGG KNPDPWAKNL NEKDYELLCL DGTRKPVEEY ANCHLARAPN HAVVTRKDKE ACVHKILRQQ QHLFGSNVTD CSGNFCL FR SETKDLLFRD DTVCLAKLHD RNTYEKYLGE EYVKAVGNLR KCSTSSLLEA CTFRRP

UniProtKB: Serotransferrin

-
Macromolecule #2: Transferrin-binding protein A

MacromoleculeName: Transferrin-binding protein A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria gonorrhoeae (bacteria)
Molecular weightTheoretical: 102.036523 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHHHHH ENLYFQGAME NVQAGQAQEK QLDTIQVKAK KQKTRRDNEV TGLGKLVKTA DTLSKEQVLD IRDLTRYDPG IAVVEQGRG ASSGYSIRGM DKNRVSLTVD GLAQIQSYTA QAALGGTRTA GSSGAINEIE YENVKAVEIS KGSNSVEQGS G ALAGSVAF ...String:
HHHHHHHHHH ENLYFQGAME NVQAGQAQEK QLDTIQVKAK KQKTRRDNEV TGLGKLVKTA DTLSKEQVLD IRDLTRYDPG IAVVEQGRG ASSGYSIRGM DKNRVSLTVD GLAQIQSYTA QAALGGTRTA GSSGAINEIE YENVKAVEIS KGSNSVEQGS G ALAGSVAF QTKTADDVIG EGRQWGIQSK TAYSGKNRGL TQSIALAGRI GGAEALLIRT GRHAGEIRAH EAAGRGVQSF NR LAPVDDG SKYAYFIVEE ECKNGGHEKC KANPKKDVVG EDKRQTVSTR DYTGPNRFLA DPLSYESRSW LFRPGFRFEN KRH YIGGIL ERTQQTFDTR DMTVPAFLTK AVFDANQKQA GSLRGNGKYA GNHKYGGLFT SGENNAPVGA EYGTGVFYDE THTK SRYGL EYVYTNADKD TWADYARLSY DRQGIGLDNH FQQTHCSADG SDKYCRPSAD KPFSYYKSDR VIYGESHKLL QAAFK KSFD TAKIRHNLSV NLGYDRFGSN LRHQDYYYQS ANRAYSLKTP PQNNGKKTSP NGREKNPYWV SIGRGNVVTR QICLFG NNT YTDCTPRSIN GKSYYAAVRD NVRLGRWADV GAGLRYDYRS THSDDGSVST GTHRTLSWNA GIVLKPADWL DLTYRTS TG FRLPSFAEMY GWRSGDKIKA VKIDPEKSFN KEAGIVFKGD FGNLEASWFN NAYRDLIVRG YEAQIKDGKE QVKGNPAY L NAQSARITGI NILGKIDWNG VWDKLPEGWY STFAYNRVRV RDIKKRADRT DIQSHLFDAI QPSRYVVGSG YDQPEGKWG VNGMLTYSKA KEITELLGSR ALLNGNSRNT KATARRTRPW YIVDVSGYYT VKKHFTLRAG VYNLLNHRYV TWENVRQTAA GAVNQHKNV GVYNRYAAPG RNYTFSLEMK F

UniProtKB: Transferrin-binding protein A

-
Macromolecule #3: Transferrin-binding protein B

MacromoleculeName: Transferrin-binding protein B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria)
Molecular weightTheoretical: 75.484914 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MCLGGGGSFD LDSVDTEAPR PAPKYQDVFS EKPQAQKDQG GYGFAMRLKR RNWYPQAKED EVKLDESDWE ATGLPDEPKE LPKRQKSVI EKVETDSDNN IYSSPYLKPS NHQNGNTGNG INQPKNQAKD YENFKYVYSG WFYKHAKREF NLKVEPKSAK N GDDGYIFY ...String:
MCLGGGGSFD LDSVDTEAPR PAPKYQDVFS EKPQAQKDQG GYGFAMRLKR RNWYPQAKED EVKLDESDWE ATGLPDEPKE LPKRQKSVI EKVETDSDNN IYSSPYLKPS NHQNGNTGNG INQPKNQAKD YENFKYVYSG WFYKHAKREF NLKVEPKSAK N GDDGYIFY HGKEPSRQLP ASGKITYKGV WHFATDTKKG QKFREIIQPS KSQGDRYSGF SGDDGEEYSN KNKSTLTDGQ EG YGFTSNL EVDFHNKKLT GKLIRNNANT DNNQATTTQY YSLEAQVTGN RFNGKATATD KPQQNSETKE HPFVSDSSSL SGG FFGPQG EELGFRFLSD DQKVAVVGSA KTKDKPANGN TAAASGGTDA AASNGAAGTS SENGKLTTVL DAVELKLGDK KVQK LDNFS NAAQLVVDGI MIPLLPEASE SGNNQANQGT NGGTAFTRKF DHTPESDKKD AQAGTQTNGA QTASNTAGDT NGKTK TYEV EVCCSNLNYL KYGMLTRKNS KSAMQAGESS SQADAKTEQV EQSMFLQGER TDEKEIPSEQ NIVYRGSWYG YIANDK STS WSGNASNATS GNRAEFTVNF ADKKITGTLT ADNRQEATFT IDGNIKDNGF EGTAKTAESG FDLDQSNTTR TPKAYIT DA KVQGGFYGPK AEELGGWFAY PGDKQTKNAT NASGNSSATV VFGAKRQQPV Q

UniProtKB: Transferrin-binding protein B

-
Macromolecule #4: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

-
Macromolecule #5: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

-
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: 53.52 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

Particle selectionNumber selected: 2588171
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3v89

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 30000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9yz4:
Neisseria gonorrhoeae Transferrin Binding Protein A in complex with Transferrin Binding Protein B and transferrin (iron bound in N lobe only)

+
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