[English] 日本語
Yorodumi
- PDB-9pgy: Crystal structure of STEAP2 N-domain in complex with NADPH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9pgy
TitleCrystal structure of STEAP2 N-domain in complex with NADPH
ComponentsMetalloreductase STEAP2
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


copper ion import across plasma membrane / Oxidoreductases; Oxidizing metal ions; With NAD+ or NADP+ as acceptor / ferric-chelate reductase (NADPH) activity / iron ion import across plasma membrane / cupric reductase (NADH) activity / copper ion import / regulated exocytosis / trans-Golgi network transport vesicle / Golgi to plasma membrane transport / response to hormone ...copper ion import across plasma membrane / Oxidoreductases; Oxidizing metal ions; With NAD+ or NADP+ as acceptor / ferric-chelate reductase (NADPH) activity / iron ion import across plasma membrane / cupric reductase (NADH) activity / copper ion import / regulated exocytosis / trans-Golgi network transport vesicle / Golgi to plasma membrane transport / response to hormone / endocytosis / early endosome / endosome membrane / endosome / Golgi membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
: / Ferric reductase transmembrane component-like domain / Ferric reductase like transmembrane component / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-NDP / Metalloreductase STEAP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsShin, I. / Liu, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA247379 United States
CitationJournal: To Be Published
Title: Crystal Structure of STEAP2 N-Domain with Its Bound NADPH Redox State Validated by Single-Crystal Spectroscopy
Authors: Shin, I. / Liu, A.
History
DepositionJul 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metalloreductase STEAP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4587
Polymers20,2661
Non-polymers1,1926
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.218, 68.218, 95.398
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-538-

HOH

31A-570-

HOH

-
Components

#1: Protein Metalloreductase STEAP2 / Prostate cancer-associated protein 1 / Protein up-regulated in metastatic prostate cancer / PUMPCn ...Prostate cancer-associated protein 1 / Protein up-regulated in metastatic prostate cancer / PUMPCn / Six-transmembrane epithelial antigen of prostate 2 / SixTransMembrane protein of prostate 1


Mass: 20266.256 Da / Num. of mol.: 1 / Mutation: F65S, F69S, W102S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STEAP2, PCANAP1, STAMP1, UNQ6507/PRO23203 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8NFT2, Oxidoreductases; Oxidizing metal ions; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5, 2.0 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 37869 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 20.41 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.031 / Rrim(I) all: 0.099 / Χ2: 1.008 / Net I/σ(I): 7.2 / Num. measured all: 364703
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.55-1.58101.80818320.4710.80.591.9030.679100
1.58-1.61101.7318820.510.8220.5631.820.71100
1.61-1.64101.34718630.6120.8710.441.4180.693100
1.64-1.679.91.1518880.7160.9130.3771.2110.704100
1.67-1.719.70.94718620.7580.9280.3150.9990.715100
1.71-1.759.30.75618830.8220.950.2590.80.897100
1.75-1.798.60.55218600.8770.9670.1980.5870.76100
1.79-1.849.90.46318780.9320.9820.1530.4880.79100
1.84-1.89100.4118800.9390.9840.1340.4321.092100
1.89-1.958.80.37318640.9530.9880.1320.3961.35999.9
1.95-2.0210.20.2418850.980.9950.0780.2530.967100
2.02-2.18.70.22918690.9730.9930.0820.2441.35599.9
2.1-2.2100.14919170.9910.9980.0490.1571.08599.9
2.2-2.329.10.14118760.9920.9980.050.1491.39199.9
2.32-2.469.30.10118870.9950.9990.0350.1071.17199.9
2.46-2.659.20.08118920.9970.9990.0280.0861.223100
2.65-2.9210.40.07219300.9980.9990.0230.0751.369100
2.92-3.3410.40.0519210.99910.0160.0531.198100
3.34-4.219.70.0419530.99910.0130.0421.315100
4.21-509.20.0262047110.0090.0270.73399.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data scaling
DENZOdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→29.54 Å / SU ML: 0.2292 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2457
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1996 1997 5.28 %
Rwork0.1929 35801 -
obs0.1933 37798 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.77 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 72 204 1677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751527
X-RAY DIFFRACTIONf_angle_d1.17012093
X-RAY DIFFRACTIONf_chiral_restr0.0644243
X-RAY DIFFRACTIONf_plane_restr0.0075262
X-RAY DIFFRACTIONf_dihedral_angle_d10.5031216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.42021400.42122519X-RAY DIFFRACTION99.81
1.59-1.630.3461400.31142517X-RAY DIFFRACTION99.92
1.63-1.680.27241410.262515X-RAY DIFFRACTION99.89
1.68-1.730.25751480.23062534X-RAY DIFFRACTION99.93
1.73-1.80.25191430.22232532X-RAY DIFFRACTION99.96
1.8-1.870.23991430.19922520X-RAY DIFFRACTION99.85
1.87-1.950.24281430.23922518X-RAY DIFFRACTION99.51
1.95-2.060.18931400.18182561X-RAY DIFFRACTION100
2.06-2.180.19841410.18482526X-RAY DIFFRACTION99.85
2.19-2.350.18511400.16972568X-RAY DIFFRACTION99.96
2.35-2.590.1871420.18712553X-RAY DIFFRACTION99.96
2.59-2.960.1831410.18742616X-RAY DIFFRACTION100
2.97-3.730.18081430.17762590X-RAY DIFFRACTION99.96
3.74-29.540.17451520.1722732X-RAY DIFFRACTION99.83

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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