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- PDB-2vq3: Crystal Structure of the Membrane Proximal Oxidoreductase Domain ... -

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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 / ferric-chelate reductase (NADPH) activity / cupric reductase (NADH) activity / copper ion import / Transferrin endocytosis and recycling / RHOD GTPase cycle / RHOF GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release ...Oxidoreductases; Oxidizing metal ions; With NAD+ or NADP+ as acceptor / ferric-chelate reductase (NADPH) activity / cupric reductase (NADH) activity / copper ion import / Transferrin endocytosis and recycling / RHOD GTPase cycle / RHOF GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / CDC42 GTPase cycle / protein secretion / multivesicular body / FAD binding / iron ion transport / endosome membrane / endosome / apoptotic process / heme binding / metal ion binding / identical protein 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)

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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


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


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


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

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Experimental details

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Experiment

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

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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

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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

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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

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