6HD1 | pdb_00006hd1

human STEAP4 bound to NADPH, FAD and heme.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6HD1

This is version 1.5 of the entry. See complete history

Literature

Cryo-EM structures of human STEAP4 reveal mechanism of iron(III) reduction.

Oosterheert, W.van Bezouwen, L.S.Rodenburg, R.N.P.Granneman, J.Forster, F.Mattevi, A.Gros, P.

(2018) Nat Commun 9: 4337-4337

  • DOI: https://doi.org/10.1038/s41467-018-06817-7
  • Primary Citation Related Structures: 
    6HCY, 6HD1

  • PubMed Abstract: 

    Enzymes of the six-transmembrane epithelial antigen of the prostate (STEAP) family reduce Fe 3+ and Cu 2+ ions to facilitate metal-ion uptake by mammalian cells. STEAPs are highly upregulated in several types of cancer, making them potential therapeutic targets. However, the structural basis for STEAP-catalyzed electron transfer through an array of cofactors to metals at the membrane luminal side remains elusive. Here, we report cryo-electron microscopy structures of human STEAP4 in absence and presence of Fe 3+ -NTA. Domain-swapped, trimeric STEAP4 orients NADPH bound to a cytosolic domain onto axially aligned flavin-adenine dinucleotide (FAD) and a single b-type heme that cross the transmembrane-domain to enable electron transfer. Substrate binding within a positively charged ring indicates that iron gets reduced while in complex with its chelator. These molecular principles of iron reduction provide a basis for exploring STEAPs as therapeutic targets.


  • Organizational Affiliation
    • Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 164.31 kDa 
  • Atom Count: 11,007 
  • Modeled Residue Count: 1,308 
  • Deposited Residue Count: 1,377 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metalloreductase STEAP4A [auth C],
B [auth A],
C [auth B]
459Homo sapiensMutation(s): 0 
Gene Names: STEAP4STAMP2TNFAIP9
EC: 1.16.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q687X5 (Homo sapiens)
Explore Q687X5 
Go to UniProtKB:  Q687X5
PHAROS:  Q687X5
GTEx:  ENSG00000127954 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ687X5
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q687X5-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
(Subject of Investigation/LOI)

Query on FAD



Download:Ideal Coordinates CCD File
F [auth C],
K [auth A],
P [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAP
(Subject of Investigation/LOI)

Query on NAP



Download:Ideal Coordinates CCD File
D [auth C],
I [auth A],
N [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
HEM
(Subject of Investigation/LOI)

Query on HEM



Download:Ideal Coordinates CCD File
E [auth C],
J [auth A],
O [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
44E

Query on 44E



Download:Ideal Coordinates CCD File
H [auth C],
M [auth A],
R [auth B]
(2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate
C15 H29 O8 P
SFZZRGHNPILUOD-CYBMUJFWSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
G [auth C],
L [auth A],
Q [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1b1

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific ResearchNetherlands731.015.201
European UnionNetherlands653706
Italian Association for Cancer ResearchItalyIG19808

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-12-11
    Changes: Other
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2024-11-13
    Changes: Data collection, Database references, Structure summary