3VE1 | pdb_00003ve1

The 2.9 angstrom crystal structure of Transferrin binding protein B (TbpB) from serogroup B M982 Neisseria meningitidis in complex with human transferrin

PDB DOI: https://doi.org/10.2210/pdb3VE1/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Neisseria meningitidis serogroup B, Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-01-06 Released: 2012-02-22
Deposition Author(s): Calmettes, C., Moraes, T.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.96 Å
R-Value Free:
0.249 (Depositor), 0.245 (DCC)
R-Value Work:
0.207 (Depositor), 0.203 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The structural basis of transferrin sequestration by transferrin-binding protein B.

Calmettes, C., Alcantara, J., Yu, R.H., Schryvers, A.B., Moraes, T.F.

(2012) Nat Struct Mol Biol 19: 358-360

PubMed: 22343719 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.2251
Primary Citation Related Structures:
3VE1, 3VE2

PubMed Abstract:
Neisseria meningitidis, the causative agent of bacterial meningitis, acquires the essential element iron from the host glycoprotein transferrin during infection through a surface transferrin receptor system composed of proteins TbpA and TbpB. Here we present the crystal structures of TbpB from N. meningitidis in its apo form and in complex with human transferrin. The structure reveals how TbpB sequesters and initiates iron release from human transferrin.

Organizational Affiliation

Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.

Macromolecule Content

Total Structure Weight: 294.82 kDa
Atom Count: 19,274
Modeled Residue Count: 2,425
Deposited Residue Count: 2,674
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transferrin-binding protein 2	A, C	658	Neisseria meningitidis serogroup B	Mutation(s): 0 Gene Names: tbpB, tbp2
UniProt
Find proteins for Q09057 (Neisseria meningitidis serogroup B) Explore Q09057 Go to UniProtKB: Q09057
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q09057
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serotransferrin	B, D	679	Homo sapiens	Mutation(s): 0 Gene Names: TF, PRO1400
UniProt & NIH Common Fund Data Resources
Find proteins for P02787 (Homo sapiens) Explore P02787 Go to UniProtKB: P02787
PHAROS: P02787 GTEx: ENSG00000091513
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02787
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain S [auth D]	E [auth A] F [auth A] I [auth B] J [auth B] K [auth B] E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth C], R [auth D], S [auth D], T [auth D], U [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D]
CO3 Query on CO3 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain P [auth D] MOL2 format, chain G [auth B] MOL2 format, chain P [auth D] mmCIF format, chain G [auth B] mmCIF format, chain P [auth D]	G [auth B], P [auth D]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Focus chain P [auth D] Interactions & Density Focus chain G [auth B] Focus chain P [auth D]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain Q [auth D] MOL2 format, chain H [auth B] MOL2 format, chain Q [auth D] mmCIF format, chain H [auth B] mmCIF format, chain Q [auth D]	H [auth B], Q [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain Q [auth D] Interactions & Density Focus chain H [auth B] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.96 Å
R-Value Free: 0.249 (Depositor), 0.245 (DCC)
R-Value Work: 0.207 (Depositor), 0.203 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.023	α = 90
b = 153.509	β = 90
c = 169.511	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-02-22

Deposition Author(s):

Calmettes, C.

Moraes, T.F.

Revision History (Full details and data files)

Version 1.0: 2012-02-22
Type: Initial release
Version 1.1: 2012-09-05
Changes: Database references
Version 1.2: 2013-09-18
Changes: Derived calculations
Version 1.3: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary

3VE1 | pdb_00003ve1

The 2.9 angstrom crystal structure of Transferrin binding protein B (TbpB) from serogroup B M982 Neisseria meningitidis in complex with human transferrin

Literature

The structural basis of transferrin sequestration by transferrin-binding protein B.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources