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- EMDB-49421: The cryo-EM structure of NmTbpA and NmTbpB in a complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-49421
TitleThe cryo-EM structure of NmTbpA and NmTbpB in a complex
Map data
Sample
  • Complex: NmTbpA/NmTbpB
    • Complex: NmTbpA
      • Protein or peptide: Transferrin-binding protein A
    • Complex: NmTbpB
    • Protein or peptide: Transferrin-binding protein B
KeywordsNeisseria outer membrane protein / Ton B dependent transporter / lipo protein / iron transport / MEMBRANE PROTEIN
Function / homology
Function and homology information


ferric iron transmembrane transporter activity / siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / cell outer membrane / cell surface
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. / 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 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel
Similarity search - Domain/homology
Transferrin-binding protein B / Transferrin-binding protein A
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria) / Neisseria meningitidis serogroup B (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsDubey SD / Noinaj N
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127884 United States
CitationJournal: To Be Published
Title: The cryo-EM structure of NmTbpA and NmTbpB in a complex
Authors: Dubey SD / Noinaj N
History
DepositionFeb 25, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49421.png

Downloads & links

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Map

FileDownload / File: emd_49421.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 420 pix.
= 354.48 Å		0.84 Å/pix.
x 420 pix.
= 354.48 Å		0.84 Å/pix.
x 420 pix.
= 354.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.239
Minimum - Maximum-0.42526758 - 0.92890537
Average (Standard dev.)0.00021504893 (±0.027705677)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 354.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49421_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49421_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NmTbpA/NmTbpB

EntireName: NmTbpA/NmTbpB
Components
  • Complex: NmTbpA/NmTbpB
    • Complex: NmTbpA
      • Protein or peptide: Transferrin-binding protein A
    • Complex: NmTbpB
    • Protein or peptide: Transferrin-binding protein B

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Supramolecule #1: NmTbpA/NmTbpB

SupramoleculeName: NmTbpA/NmTbpB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Neisseria meningitidis (bacteria)
Molecular weightTheoretical: 80 KDa

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Supramolecule #2: NmTbpA

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

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Supramolecule #3: NmTbpB

SupramoleculeName: NmTbpB / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Neisseria meningitidis (bacteria)

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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 (E. coli)
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

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Macromolecule #2: Transferrin-binding protein B

MacromoleculeName: Transferrin-binding protein B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria)
Molecular weightTheoretical: 77.939453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHDYDI PTTENLYFQG AMLGGGGSFD LDSVDTEAPR PAPKYQDVFS EKPQAQKDQG GYGFAMRLKR RNWYPQAKED EVKLDESDW EATGLPDEPK ELPKRQKSVI EKVETDSDNN IYSSPYLKPS NHQNGNTGNG INQPKNQAKD YENFKYVYSG W FYKHAKRE ...String:
HHHHHHDYDI PTTENLYFQG AMLGGGGSFD LDSVDTEAPR PAPKYQDVFS EKPQAQKDQG GYGFAMRLKR RNWYPQAKED EVKLDESDW EATGLPDEPK ELPKRQKSVI EKVETDSDNN IYSSPYLKPS NHQNGNTGNG INQPKNQAKD YENFKYVYSG W FYKHAKRE FNLKVEPKSA KNGDDGYIFY HGKEPSRQLP ASGKITYKGV WHFATDTKKG QKFREIIQPS KSQGDRYSGF SG DDGEEYS NKNKSTLTDG QEGYGFTSNL EVDFHNKKLT GKLIRNNANT DNNQATTTQY YSLEAQVTGN RFNGKATATD KPQ QNSETK EHPFVSDSSS LSGGFFGPQG EELGFRFLSD DQKVAVVGSA KTKDKPANGN TAAASGGTDA AASNGAAGTS SENG KLTTV LDAVELKLGD KKVQKLDNFS NAAQLVVDGI MIPLLPEASE SGNNQANQGT NGGTAFTRKF DHTPESDKKD AQAGT QTNG AQTASNTAGD TNGKTKTYEV EVCCSNLNYL KYGMLTRKNS KSAMQAGESS SQADAKTEQV EQSMFLQGER TDEKEI PSE QNIVYRGSWY GYIANDKSTS WSGNASNATS GNRAEFTVNF ADKKITGTLT ADNRQEATFT IDGNIKDNGF EGTAKTA ES GFDLDQSNTT RTPKAYITDA KVQGGFYGPK AEELGGWFAY PGDKQTKNAT NASGNSSATV VFGAKRQQPV Q

UniProtKB: Transferrin-binding protein B

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridMaterial: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.5 e/Å2
Electron beamAcceleration voltage: 1200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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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 / Number images used: 38789
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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