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- EMDB-0199: human STEAP4 bound to NADP, FAD, heme and Fe(III)-NTA. -

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Basic information

Entry
Database: EMDB / ID: 0199
Titlehuman STEAP4 bound to NADP, FAD, heme and Fe(III)-NTA.
Map data
SampleHuman Six-Transmembrane Epithelial Antigen of the Prostate 4:
Metalloreductase STEAP4 / (ligand) x 5
Function / homologyFerric reductase like transmembrane component / NADP oxidoreductase coenzyme F420-dependent / NAD(P)-binding domain superfamily / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / Ferric reductase transmembrane component-like domain / ferric-chelate reductase (NADPH) activity / cupric reductase activity / With NAD or NADP as acceptor / iron ion import across cell outer membrane / copper ion import ...Ferric reductase like transmembrane component / NADP oxidoreductase coenzyme F420-dependent / NAD(P)-binding domain superfamily / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / Ferric reductase transmembrane component-like domain / ferric-chelate reductase (NADPH) activity / cupric reductase activity / With NAD or NADP as acceptor / iron ion import across cell outer membrane / copper ion import / fat cell differentiation / early endosome membrane / iron ion homeostasis / endosome / Golgi membrane / integral component of plasma membrane / Golgi apparatus / extracellular exosome / plasma membrane / metal ion binding / Metalloreductase STEAP4
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.1 Å resolution
AuthorsOosterheert W / van Bezouwen LS / Rodenburg RNP / Forster F / Mattevi A / Gros P
CitationJournal: Nat Commun / Year: 2018
Title: Cryo-EM structures of human STEAP4 reveal mechanism of iron(III) reduction.
Authors: Wout Oosterheert / Laura S van Bezouwen / Remco N P Rodenburg / Joke Granneman / Friedrich Förster / Andrea Mattevi / Piet Gros
Validation ReportPDB-ID: 6hcy

SummaryFull reportAbout validation report
DateDeposition: Aug 17, 2018 / Header (metadata) release: Oct 24, 2018 / Map release: Oct 24, 2018 / Last update: Oct 31, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.053
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.053
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6hcy
  • Surface level: 0.053
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0199.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
0.81 Å/pix.
= 243.81 Å
300 pix
0.81 Å/pix.
= 243.81 Å
300 pix
0.81 Å/pix.
= 243.81 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8127 Å
Density
Contour Level:0.053 (by author), 0.053 (movie #1):
Minimum - Maximum-0.13904265 - 0.22599746
Average (Standard dev.)0.0004582962 (0.0058541913)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin0.00.00.0
Limit299.0299.0299.0
Spacing300300300
CellA=B=C: 243.81 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.81270.81270.8127
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z243.810243.810243.810
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1390.2260.000

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Supplemental data

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Mask #1

Fileemd_0199_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Human Six-Transmembrane Epithelial Antigen of the Prostate 4

EntireName: Human Six-Transmembrane Epithelial Antigen of the Prostate 4
Number of components: 7

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Component #1: protein, Human Six-Transmembrane Epithelial Antigen of the Prostate 4

ProteinName: Human Six-Transmembrane Epithelial Antigen of the Prostate 4
Recombinant expression: No
MassTheoretical: 152 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Vector: pUPE 3423 / Strain: HEK293 GNTI- / Cell of expression system: HEK293 GNTI-

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Component #2: protein, Metalloreductase STEAP4

ProteinName: Metalloreductase STEAP4 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 52.036 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

LigandName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.743405 kDa

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Component #4: ligand, PROTOPORPHYRIN IX CONTAINING FE

LigandName: PROTOPORPHYRIN IX CONTAINING FE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.616487 kDa

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Component #5: ligand, FLAVIN-ADENINE DINUCLEOTIDE

LigandName: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide
Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.78555 kDa

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Component #6: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #7: ligand, (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate

LigandName: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.36836 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 4 mg/ml
Buffer solution: 25 mM MES pH 5.5 200 mM NaCl 0.08% (w/v) digitonin
pH: 5.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 % / Details: Blotted for 4 seconds Blotforce 0.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Details: Grid was prescreened on a 200 kV Talos Arctica Microscope. Microscope alignment was performed by Wim Hagen at EMBL Heidelberg.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 47.4 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 165000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 2000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 8211

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 255144 / Details: Titan Krios at EMBL Heidelberg.
3D reconstructionSoftware: RELION / CTF correction: GCTF within the Relion GUI. / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Standard Refinement ant Post processing in Relion.
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Details: No Fitting was performed.
Output model

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