6XR0 | pdb_00006xr0

Crystal Structure of Human Melanotransferrin in complex with SC57.32 Fab

• PDB DOI: https://doi.org/10.2210/pdb6XR0/pdb

• Classification: METAL TRANSPORT
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2020-07-10 Released: 2021-01-20 
• Deposition Author(s): Hayashi, K., Longenecker, K.L., Vivona, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.06 Å
• R-Value Free: 
  0.225 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Complex of human Melanotransferrin and SC57.32 Fab fragment reveals novel interdomain arrangement with ferric N-lobe and open C-lobe.

Hayashi, K., Longenecker, K.L., Liu, L.Y., Faust, B., Prashar, A., Hampl, J., Stoll, V., Vivona, S.

(2021) Sci Rep 11: 566

• DOI: https://doi.org/10.1038/s41598-020-79090-8

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 129.05 kDa 
• Atom Count: 8,704 
• Modeled Residue Count: 1,112 
• Deposited Residue Count: 1,173 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SC57.32 Fab Heavy Chain	A [auth H]	221	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SC57.32 Fab Light Chain	B [auth L]	214	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Melanotransferrin	C [auth M]	738	Homo sapiens	Mutation(s): 0  Gene Names: MELTF, MAP97, MFI2
UniProt & NIH Common Fund Data Resources
Find proteins for P08582 (Homo sapiens) Explore P08582  Go to UniProtKB:  P08582
PHAROS:  P08582 GTEx:  ENSG00000163975
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P08582-1

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A], E [auth B]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth M]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BCT	J [auth M]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE (Subject of Investigation/LOI)	I [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG	G [auth M]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	H [auth M]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.06 Å
• R-Value Free:  0.225 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.829	α = 90
b = 136.91	β = 91.46
c = 111.135	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-20 
Deposition Author(s): Hayashi, K., Longenecker, K.L., Vivona, S.

Revision History  

• Version 1.0: 2021-01-20
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary