3V8X

The crystal structure of transferrin binding protein A (TbpA) from Neisserial meningitidis serogroup B in complex with full length human transferrin

• PDB DOI: https://doi.org/10.2210/pdb3V8X/pdb

• Classification: MEMBRANE PROTEIN/METAL TRANSPORT
• Organism(s): Neisseria meningitidis serogroup B, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2011-12-23 Released: 2012-02-29 
• Deposition Author(s): Noinaj, N., Easley, N., Buchanan, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.267 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 182.68 kDa 
• Atom Count: 12,233 
• Modelled Residue Count: 1,529 
• Deposited Residue Count: 1,602 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transferrin-binding protein 1	A	904	Neisseria meningitidis serogroup B	Mutation(s): 2  Gene Names: tbp1, NMB0461 Membrane Entity: Yes
UniProt
Find proteins for Q9K0U9 (Neisseria meningitidis serogroup B (strain MC58)) Explore Q9K0U9  Go to UniProtKB:  Q9K0U9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serotransferrin	B	698	Homo sapiens	Mutation(s): 1  Gene Names: TF, PRO1400 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P02787 (Homo sapiens) Explore P02787  Go to UniProtKB:  P02787
PHAROS:  P02787 GTEx:  ENSG00000091513

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	10		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G98736SM GlyCosmos:  G98736SM GlyGen:  G98736SM

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	9		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G74608QW GlyCosmos:  G74608QW GlyGen:  G74608QW

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C8E	E [auth A], F [auth A]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C16 H34 O5 FEOZZFHAVXYAMB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.267 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.014	α = 90
b = 129.362	β = 90
c = 198.589	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-29 
Deposition Author(s): Noinaj, N., Easley, N., Buchanan, S.K.

Revision History  

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2012-04-18
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary