[English] 日本語
Yorodumi
- EMDB-0200: human STEAP4 bound to NADPH, FAD and heme. -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 0200
Titlehuman STEAP4 bound to NADPH, FAD and heme.
Map data
Samplehomotrimer of human STEAP4.:
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 / 3.8 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: 6hd1

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

-
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-6hd1
  • Surface level: 0.053
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_0200.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.03 Å/pix.
= 246.84 Å
240 pix
1.03 Å/pix.
= 246.84 Å
240 pix
1.03 Å/pix.
= 246.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0285 Å
Density
Contour Level:0.053 (by author), 0.053 (movie #1):
Minimum - Maximum-0.095823534 - 0.22453356
Average (Standard dev.)0.000767484 (0.0055400585)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin0.00.00.0
Limit239.0239.0239.0
Spacing240240240
CellA=B=C: 246.84 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.02851.02851.0285
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z246.840246.840246.840
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0960.2250.001

-
Supplemental data

-
Mask #1

Fileemd_0200_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

-
Sample components

+
Entire homotrimer of human STEAP4.

EntireName: homotrimer of human STEAP4. / Number of components: 7

+
Component #1: protein, homotrimer of human STEAP4.

ProteinName: homotrimer of human STEAP4. / Recombinant expression: No
MassTheoretical: 152 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Vector: pUPE 3423 / Cell of expression system: HEK293 GNTI-

+
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)

+
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

+
Component #4: ligand, PROTOPORPHYRIN IX CONTAINING FE

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

+
Component #5: ligand, FLAVIN-ADENINE DINUCLEOTIDE

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

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

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

+
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

-
Experimental details

-
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% digitonin (w/v)
pH: 5.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 % / Details: blot time 4seconds blot force 0.

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Details: 200 kV Talos Arctica at Utrecht University, the Netherlands.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 45.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 3000.0 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 2321

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 209075
3D reconstructionSoftware: RELION / CTF correction: performed in GCTF. / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Details: performed by RELION.
FSC plot
(resolution estimation)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more