1CX8 | pdb_00001cx8

CRYSTAL STRUCTURE OF THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR

PDB DOI: https://doi.org/10.2210/pdb1CX8/pdb

Classification: METAL TRANSPORT
Organism(s): Homo sapiens
Expression System: Cricetinae gen. sp.
Mutation(s): No

Deposited: 1999-08-28 Released: 1999-09-09
Deposition Author(s): Lawrence, C.M., Ray, S., Babyonyshev, M., Galluser, R., Borhani, D., Harrison, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.284 (Depositor)
R-Value Work:
0.243 (Depositor), 0.268 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of the ectodomain of human transferrin receptor.

Lawrence, C.M., Ray, S., Babyonyshev, M., Galluser, R., Borhani, D.W., Harrison, S.C.

(1999) Science 286: 779-782

PubMed: 10531064 Search on PubMed
DOI: https://doi.org/10.1126/science.286.5440.779
Primary Citation Related Structures:
1CX8

PubMed Abstract:
The transferrin receptor (TfR) undergoes multiple rounds of clathrin-mediated endocytosis and reemergence at the cell surface, importing iron-loaded transferrin (Tf) and recycling apotransferrin after discharge of iron in the endosome. The crystal structure of the dimeric ectodomain of the human TfR, determined here to 3.2 angstroms resolution, reveals a three-domain subunit. One domain closely resembles carboxy- and aminopeptidases, and features of membrane glutamate carboxypeptidase can be deduced from the TfR structure. A model is proposed for Tf binding to the receptor.

Organizational Affiliation

Howard Hughes Medical Institute and Children's Hospital Laboratory of Molecular Medicine, 320 Longwood Avenue, Boston, MA 02115, USA.

Macromolecule Content

Total Structure Weight: 581.9 kDa
Atom Count: 40,808
Modeled Residue Count: 5,112
Deposited Residue Count: 5,112
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSFERRIN RECEPTOR PROTEIN	A, B, C, D, E A, B, C, D, E, F, G, H	639	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02786 (Homo sapiens) Explore P02786 Go to UniProtKB: P02786
PHAROS: P02786 GTEx: ENSG00000072274
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02786
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H	Go to GlyGen: P02786-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain MA [auth F] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain OA [auth F] SDF format, chain Q [auth B] SDF format, chain SA [auth G] SDF format, chain TA [auth G] SDF format, chain U [auth C] SDF format, chain UA [auth G] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain YA [auth H] SDF format, chain ZA [auth H] SDF format, chain P [auth B] SDF format, chain I [auth A] SDF format, chain AA [auth D] MOL2 format, chain AB [auth H] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain SA [auth G] MOL2 format, chain TA [auth G] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth G] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain YA [auth H] MOL2 format, chain ZA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain AB [auth H] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain IA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain NA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain SA [auth G] mmCIF format, chain TA [auth G] mmCIF format, chain U [auth C] mmCIF format, chain UA [auth G] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain YA [auth H] mmCIF format, chain ZA [auth H] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain AA [auth D]	AA [auth D] AB [auth H] BA [auth D] CA [auth D] GA [auth E] AA [auth D], AB [auth H], BA [auth D], CA [auth D], GA [auth E], HA [auth E], I [auth A], IA [auth E], J [auth A], K [auth A], MA [auth F], NA [auth F], O [auth B], OA [auth F], P [auth B], Q [auth B], SA [auth G], TA [auth G], U [auth C], UA [auth G], V [auth C], W [auth C], YA [auth H], ZA [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain AB [auth H] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain U [auth C] Focus chain UA [auth G] Focus chain V [auth C] Focus chain W [auth C] Focus chain YA [auth H] Focus chain ZA [auth H] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth H] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain U [auth C] Focus chain UA [auth G] Focus chain V [auth C] Focus chain W [auth C] Focus chain YA [auth H] Focus chain ZA [auth H]
SM Query on SM Download:Ideal Coordinates CCD File SDF format, chain BB [auth H] SDF format, chain CB [auth H] SDF format, chain DA [auth D] SDF format, chain DB [auth H] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain PA [auth F] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain VA [auth G] SDF format, chain WA [auth G] SDF format, chain X [auth C] SDF format, chain XA [auth G] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain N [auth A] SDF format, chain LA [auth E] MOL2 format, chain BB [auth H] MOL2 format, chain CB [auth H] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain VA [auth G] MOL2 format, chain WA [auth G] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth G] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain N [auth A] MOL2 format, chain LA [auth E] mmCIF format, chain BB [auth H] mmCIF format, chain CB [auth H] mmCIF format, chain DA [auth D] mmCIF format, chain DB [auth H] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain PA [auth F] mmCIF format, chain QA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain VA [auth G] mmCIF format, chain WA [auth G] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth G] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain N [auth A] mmCIF format, chain LA [auth E]	BB [auth H] CB [auth H] DA [auth D] DB [auth H] EA [auth D] BB [auth H], CB [auth H], DA [auth D], DB [auth H], EA [auth D], FA [auth D], JA [auth E], KA [auth E], L [auth A], LA [auth E], M [auth A], N [auth A], PA [auth F], QA [auth F], R [auth B], RA [auth F], S [auth B], T [auth B], VA [auth G], WA [auth G], X [auth C], XA [auth G], Y [auth C], Z [auth C]	SAMARIUM (III) ION Sm DOSGOCSVHPUUIA-UHFFFAOYSA-N		Interactions Focus chain BB [auth H] Focus chain CB [auth H] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain T [auth B] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain X [auth C] Focus chain XA [auth G] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain BB [auth H] Focus chain CB [auth H] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain T [auth B] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain X [auth C] Focus chain XA [auth G] Focus chain Y [auth C] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.284 (Depositor)
R-Value Work: 0.243 (Depositor), 0.268 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.4	α = 90
b = 216.9	β = 90
c = 361.9	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
DM	model building
CNS	refinement
DM	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 1999-09-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1999-09-09
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2016-12-14
Changes: Structure summary
Version 1.4: 2018-01-31
Changes: Experimental preparation
Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.6: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary