7Q1L | pdb_00007q1l

Glycosilated Human Serum Apo-tranferrin

PDB DOI: https://doi.org/10.2210/pdb7Q1L/pdb

Classification: METAL TRANSPORT
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2021-10-20 Released: 2022-03-16
Deposition Author(s): Gavira, J.A., Moreno, A., Campos-Escamilla, C., Gonzalez-Ramirez, L.A., Siliqi, D.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.249 (Depositor), 0.275 (DCC)
R-Value Work:
0.220 (Depositor)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

X-ray Characterization of Conformational Changes of Human Apo- and Holo-Transferrin.

Campos-Escamilla, C., Siliqi, D., Gonzalez-Ramirez, L.A., Lopez-Sanchez, C., Gavira, J.A., Moreno, A.

(2021) Int J Mol Sci 22

PubMed: 34948188 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/ijms222413392
Primary Citation Related Structures:
7Q1L

PubMed Abstract:
Human serum transferrin (Tf) is a bilobed glycoprotein whose function is to transport iron through receptor-mediated endocytosis. The mechanism for iron release is pH-dependent and involves conformational changes in the protein, thus making it an attractive system for possible biomedical applications. In this contribution, two powerful X-ray techniques, namely Macromolecular X-ray Crystallography (MX) and Small Angle X-ray Scattering (SAXS), were used to study the conformational changes of iron-free (apo) and iron-loaded (holo) transferrin in crystal and solution states, respectively, at three different pH values of physiological relevance. A crystallographic model of glycosylated apo-Tf was obtained at 3.0 Å resolution, which did not resolve further despite many efforts to improve crystal quality. In the solution, apo-Tf remained mostly globular in all the pH conditions tested; however, the co-existence of closed, partially open, and open conformations was observed for holo-Tf, which showed a more elongated and flexible shape overall.

Organizational Affiliation

Instituto de Química, Universidad Nacional Autónoma de Mexico, Av. Universidad 3000, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico.

Macromolecule Content

Total Structure Weight: 151.81 kDa
Atom Count: 10,716
Modeled Residue Count: 1,352
Deposited Residue Count: 1,352
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serotransferrin	A, B	676	Homo sapiens	Mutation(s): 0
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
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P02787-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth D], D [auth C]	2		N-Glycosylation	Interactions Focus chain C [auth D] Focus chain D [auth C] Interactions & Density Focus chain C [auth D] Focus chain D [auth C]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	O [auth B], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain O [auth B] Focus chain P [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B]	J [auth A], N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Interactions & Density Focus chain J [auth A] Focus chain N [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]