[English] 日本語
Yorodumi
- PDB-2vq3: Crystal Structure of the Membrane Proximal Oxidoreductase Domain ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vq3
TitleCrystal Structure of the Membrane Proximal Oxidoreductase Domain of Human Steap3, the Dominant Ferric Reductase of the Erythroid Transferrin Cycle
ComponentsMETALLOREDUCTASE STEAP3
KeywordsOXIDOREDUCTASE / METAL-BINDING / TRANSMEMBRANE / ROSSMANN FOLD / TRANSPORT / CELL CYCLE / TRANSFERRIN / FLAVOPROTEIN / ALTERNATIVE SPLICING / TRANSFERRIN RECEPTOR / FERRIREDUCTASE / FERRIC-REDUCTASE / IRON TRANSPORT / PHOSPHOPROTEIN / STEAP3 / COPPER / MEMBRANE / ENDOSOME / APOPTOSIS / TF / NAD / TFR / FAD / FNO / NADP / TFR1 / IRON / STEAP / POLYMORPHISM / GLYCOPROTEIN / ION TRANSPORT / DINUCLEOTIDE-BINDING DOMAIN
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on metal ions, NAD or NADP as acceptor / ferric-chelate reductase (NADPH) activity / cupric reductase activity / transferrin transport / copper ion import / Transferrin endocytosis and recycling / RHOF GTPase cycle / RHOD GTPase cycle / RHOJ GTPase cycle ...Oxidoreductases; Oxidizing metal ions; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on metal ions, NAD or NADP as acceptor / ferric-chelate reductase (NADPH) activity / cupric reductase activity / transferrin transport / copper ion import / Transferrin endocytosis and recycling / RHOF GTPase cycle / RHOD GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / CDC42 GTPase cycle / protein secretion / FAD binding / multivesicular body / endosome membrane / endosome / cell cycle / apoptotic process / heme binding / identical protein binding / metal ion binding / plasma membrane / cytoplasm
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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Metalloreductase STEAP3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSendamarai, A.K. / Ohgami, R.S. / Fleming, M.D. / Lawrence, C.M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structure of the Membrane Proximal Oxidoreductase Domain of Human Steap3, the Dominant Ferrireductase of the Erythroid Transferrin Cycle
Authors: Sendamarai, A.K. / Ohgami, R.S. / Fleming, M.D. / Lawrence, C.M.
#1: Journal: Nat.Genet. / Year: 2005
Title: Identification of a Ferrireductase Required for Efficient Transferrin-Dependent Iron Uptake in Erythroid Cells
Authors: Ohgami, R.S. / Campagna, D.R. / Greer, E.L. / Antiochos, B. / Mcdonald, A. / Chen, J. / Sharp, J.J. / Fujiwara, Y. / Barker, J.E. / Fleming, M.D.
#2: Journal: Blood / Year: 2005
Title: Nm1054, a Spontaneous, Recessive, Hypochromic, Microcytic Anemia Mutation in the Mouse
Authors: Ohgami, R.S. / Campagna, D.R. / Antiochos, B. / Wood, E.B. / Sharp, J.J. / Barker, J.E. / Fleming, M.D.
History
DepositionMar 10, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 2, 2022Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: METALLOREDUCTASE STEAP3
B: METALLOREDUCTASE STEAP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3105
Polymers46,6312
Non-polymers1,6793
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint1.9 kcal/mol
Surface area19340 Å2
MethodPQS
Unit cell
Length a, b, c (Å)37.686, 66.812, 143.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 0.005, -0.007), (-0.005, -0.998, 0.065), (-0.007, 0.065, 0.998)
Vector: 57.10159, -37.85538, 1.4179)

-
Components

#1: Protein METALLOREDUCTASE STEAP3 / STEAP3 DIMER WITH NADPH / SIX-TRANSMEMBRANE EPITHELIAL ANTIGEN OF PROSTATE 3 / TUMOR SUPPRESSOR- ...STEAP3 DIMER WITH NADPH / SIX-TRANSMEMBRANE EPITHELIAL ANTIGEN OF PROSTATE 3 / TUMOR SUPPRESSOR-ACTIVATED PATHWAY PROTEIN 6 / HTSAP6 / PHYDE / HPHYDE / DUDULIN-2


Mass: 23315.676 Da / Num. of mol.: 2
Fragment: NADPH/FLAVIN DEPENDENT OXIDOREDUCTASE, RESIDUES 1-215
Source method: isolated from a genetically manipulated source
Details: RESIDUES 1-215 CLONED, NADPH BOUND / Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: RENAL CELL ADENOCARCINOMA / Organ: KIDNEY / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL
References: UniProt: Q658P3, EC: 1.16.1.2, Oxidoreductases; Oxidizing metal ions; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.84 %
Description: RIGID BODY REFINED AND FURTHER REFINE FROM APO- STRUCTURE 2VNS
Crystal growpH: 5.6
Details: 0.01M FECL3, 40-100MM NA3.CITRATE, 4% V/V JEFFAMINE M600 PH5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.1271
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 11, 2007
Details: FLAT COLLIMATING MIRROR, DOUBLE CRYSTAL MONOCHROMATOR, TOROID FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 27874 / % possible obs: 97.5 % / Observed criterion σ(I): 5 / Redundancy: 3.9 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 19.1
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.8 / % possible all: 85.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKLdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VNS

2vns


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.907 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGION BETWEEN RESIDUES 159 TO 164 HAS POOR DENSITY FOR SIDE CHAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1293 5.2 %RANDOM
Rwork0.197 ---
obs0.199 23736 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--1.73 Å20 Å2
3----1.95 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2729 0 109 125 2963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222967
X-RAY DIFFRACTIONr_bond_other_d0.0010.021990
X-RAY DIFFRACTIONr_angle_refined_deg1.4982.0054055
X-RAY DIFFRACTIONr_angle_other_deg3.29534852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg38.9445374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63123.613119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86315467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2981522
X-RAY DIFFRACTIONr_chiral_restr0.0870.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023284
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02578
X-RAY DIFFRACTIONr_nbd_refined0.2370.2618
X-RAY DIFFRACTIONr_nbd_other0.2410.22002
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21444
X-RAY DIFFRACTIONr_nbtor_other0.0990.21543
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2143
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5311.52329
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67322967
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.05831278
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9254.51086
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 97
Rwork0.202 1620

+
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