3NH9

Nucleotide Binding Domain of Human ABCB6 (ATP bound structure)

• PDB DOI: https://doi.org/10.2210/pdb3NH9/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-14 Released: 2010-08-25 
• Deposition Author(s): Haffke, M., Menzel, A., Carius, Y., Jahn, D., Heinz, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.248 
• R-Value Work: 0.175 
• R-Value Observed: 0.179 

Starting Model: experimental

Literature

Structures of the nucleotide-binding domain of the human ABCB6 transporter and its complexes with nucleotides.

Haffke, M., Menzel, A., Carius, Y., Jahn, D., Heinz, D.W.

(2010) Acta Crystallogr D Biol Crystallogr 66: 979-987

• PubMed: 20823549 
• DOI: https://doi.org/10.1107/S0907444910028593
• Primary Citation of Related Structures:  
  3NH6, 3NH9, 3NHA, 3NHB


• PubMed Abstract: 
  

  The human ATP-binding cassette (ABC) transporter ABCB6 is involved in haem-precursor transport across the mitochondrial membrane. The crystal structure of its nucleotide-binding domain (NBD) has been determined in the apo form and in complexes with ADP, with ADP and Mg(2+) and with ATP at high resolution. The overall structure is L-shaped and consists of two lobes, consistent with other reported NBD structures. Nucleotide binding is mediated by the highly conserved Tyr599 and the Walker A motif, and induces notable structural changes. Structural comparison with other structurally characterized NBDs and full-length ABC transporters gives the first insight into the possible catalytic mechanism of ABCB6 and the role of the N-terminal helix alpha(1) in full-length ABCB6.

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Organizational Affiliation: 

Helmholtz Zentrum für Infektionsforschung, Braunschweig, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 34.15 kDa 
• Atom Count: 2,303 
• Modelled Residue Count: 273 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-binding cassette sub-family B member 6, mitochondrial	A	306	Homo sapiens	Mutation(s): 0  Gene Names: ABCB6, MTABC3, PRP, UMAT EC: 7.6.2.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP58 (Homo sapiens) Explore Q9NP58  Go to UniProtKB:  Q9NP58
PHAROS:  Q9NP58 GTEx:  ENSG00000115657

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
BME	C [auth A], D [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.248 
• R-Value Work: 0.175 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.152	α = 90
b = 65.626	β = 90
c = 69.522	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-25 
Deposition Author(s): Haffke, M., Menzel, A., Carius, Y., Jahn, D., Heinz, D.W.

Revision History  

• Version 1.0: 2010-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-03-21
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description