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

ID or keywords:

Entry

Database: PDB / ID: 2vns

Title

Crystal Structure of the Membrane Proximal Oxidoreductase Domain of Human Steap3, the Dominant Ferric Reductase of the Erythroid Transferrin Cycle

Components

METALLOREDUCTASE STEAP3

Keywords

OXIDOREDUCTASE / 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 ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS / Resolution: 2 Å

Authors

Sendamarai, 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.

History

Deposition	Feb 7, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 6, 2008	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	May 8, 2024	Group: Data collection / Database references / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2vns.cif.gz	150.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2vns.ent.gz	122.2 KB	Display	PDB format
PDBx/mmJSON format	2vns.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vn/2vns ftp://data.pdbj.org/pub/pdb/validation_reports/vn/2vns	HTTPS FTP

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Related structure data

Related structure data	2vq3C C: citing same article (ref.)
Similar structure data	3trs-d 3eey-4 3eey-3 1sxr-3 6iru-2 6trr-1 4hpe-5 1u90-d 2qxu-10 3lby-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#35 - Nov 2002 Ferritin and Transferrin similarity (5) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: METALLOREDUCTASE STEAP3

B: METALLOREDUCTASE STEAP3

hetero molecules

46.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

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 number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	29 - 104
2	1	1	2	B	29 - 104
1	2	1	2	A	105 - 159
2	2	1	2	B	105 - 159
1	3	1	3	A	160 - 161
2	3	1	3	B	160 - 161
1	4	1	2	A	163 - 204
2	4	1	2	B	163 - 204
1	5	1	3	A	205 - 209
2	5	1	3	B	205 - 209

NCS oper: (Code: given
Matrix: (-1, 0.002, 0.013), (-0.002, -0.998, 0.067), (0.013, 0.067, 0.998)
Vector: 55.92755, -37.84579, 0.74035)

#1: Protein	METALLOREDUCTASE STEAP3 / SIX-TRANSMEMBRANE EPITHELIAL ANTIGEN OF PROSTATE 3 / TUMOR SUPPRESSOR-ACTIVATED PATHWAY PROTEIN 6 / ...SIX-TRANSMEMBRANE EPITHELIAL ANTIGEN OF PROSTATE 3 / TUMOR SUPPRESSOR-ACTIVATED PATHWAY PROTEIN 6 / HTSAP6 / PHYDE / HPHYDE / DUDULIN-2 / STEAP3 DIMER 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 / Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: KIDNEY, RENAL CELL ADENOCARCINOMA / 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
#2: Chemical	ChemComp-CIT / CITRIC ACID / Citric acid Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 47.01 % Description: MIRAS TECHNIQUE INCLUDED MAD FROM INCORPORATED PT AND MIR USING PT AND HG DERIVATIVES
Crystal grow	pH: 5.6 Details: 0.01M FECL3, 40-100MM NA3.CITRATE AND 4% V/V JEFFAMINE M600 PH5.6

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 1.07149, 0.82654, 1.07199, 1.00545, 1.1271

Detector

Type: MARRESEARCH / Detector: CCD / Date: Mar 11, 2007
Details: FLAT COLLIMATING MIRROR, DOUBLE CRYSTAL MONOCHROMATOR, TOROID FOCUSING MIRROR

Radiation

Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.07149	1
2	0.82654	1
3	1.07199	1
4	1.00545	1
5	1.1271	1

Reflection

Resolution: 1.98→50 Å / Num. obs: 25300 / % possible obs: 96.8 % / Observed criterion σ(I): 5 / Redundancy: 3.8 % / R_merge(I) obs: 0.05 / Net I/σ(I): 16.1

Reflection shell

Resolution: 1.98→2.05 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.24 / Mean I/σ(I) obs: 3.3 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL		data reduction
SCALEPACK		data scaling
SOLVE		phasing

Refinement

Method to determine structure:

MIRAS
Starting model: NONE

Resolution: 2→50 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.929 / SU B: 8.467 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R Free: 0.177 / 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.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.244	1268	5.2 %	RANDOM
R_work	0.203	-	-	-
obs	0.205	23241	96.9 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 19.24 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	0 Å²
2-	-	1.84 Å²	0 Å²
3-	-	-	-1.84 Å²

Refinement step

Cycle: LAST / Resolution: 2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2724	0	13	136	2873

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	2820
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1911
X-RAY DIFFRACTION	r_angle_refined_deg	1.5	1.964	3837
X-RAY DIFFRACTION	r_angle_other_deg	1.406	3	4667
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	29.107	5	370
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.356	23.982	113
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.111	15	457
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.076	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.196	0.2	437
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3184
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	558
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	561
X-RAY DIFFRACTION	r_nbd_other	0.213	0.2	1942
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	1393
X-RAY DIFFRACTION	r_nbtor_other	0.082	0.2	1535
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.233	0.2	134
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.381	0.2	19
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.322	0.2	63
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.534	0.2	10
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.057	1.5	2308
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.417	2	2938
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.631	3	1132
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.86	4.5	897
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Number	Type	Rms dev position (Å)	Weight position
1053	tight positional	0.05	0.05
1200	medium positional	0.38	0.5
42	loose positional	0.64	5
1053	tight thermal	0.08	0.5
1200	medium thermal	0.41	2
42	loose thermal	1.75	10

LS refinement shell

Resolution: 2→2.05 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.293	101
R_work	0.229	1686

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.2199	-1.786	1.0616	2.7622	-0.9765	3.1887	0.0679	-0.0063	-0.0405	-0.0108	-0.0165	0.1157	0.0868	-0.1412	-0.0514	0.0848	-0.0152	-0.0139	0.1104	-0.0218	0.1003	31.5824	-26.2961	57.9569
2	5.2052	0.5487	2.1559	2.8639	0.9506	1.4102	-0.1339	-0.0037	-0.0534	0.2384	0.1381	-0.1225	0.0892	0.0411	-0.0042	0.0687	0.0194	0.011	0.1171	-0.027	0.0295	34.2473	-22.5638	64.0259
3	1.0113	-0.5435	0.1395	1.1012	0.7355	1.0915	-0.0364	0.0128	0.0455	0.0642	0.0969	-0.052	0.0571	-0.0304	-0.0605	0.0876	0.0047	-0.0028	0.0955	0.007	0.0892	38.3547	-28.5376	61.4705
4	3.3583	-0.8716	2.8566	0.857	-1.0027	2.5381	-0.0191	-0.6135	-0.0633	0.1448	-0.0705	-0.4082	0.0924	0.5556	0.0896	0.1271	0.0571	-0.0497	0.1321	-0.0437	0.069	46.5555	-35.4023	63.3242
5	1.4123	0.772	-3.2437	2.6006	-3.6539	9.0737	-0.0352	-0.0809	0.0172	-0.1115	0.0584	-0.0089	0.1165	0.0543	-0.0231	0.1057	-0.0105	-0.0057	0.0976	-0.0166	0.098	39.8787	-34.008	49.8479
6	3.4724	2.0147	-5.0768	1.169	-2.9456	7.4224	0.0597	-0.4189	0.1343	-0.0856	-0.1465	0.0116	0.512	0.5613	0.0868	0.1126	0.0241	0.0037	0.1136	-0.0144	0.0941	47.1036	-35.8794	41.7025
7	2.357	-1.5749	1.3569	1.2929	-0.6951	1.5363	0.0052	0.0219	-0.0452	0.0383	-0.0235	0.0531	0.0562	0.0473	0.0182	0.1166	-0.005	-0.0018	0.0859	-0.0071	0.1004	39.6807	-37.901	51.7852
8	11.9494	-1.7724	1.2651	5.5061	2.2757	1.2912	0.1695	0.0955	0.064	-0.4019	-0.0976	0.4109	-0.1814	0.1416	-0.0718	0.0932	-0.0205	-0.011	0.0887	0.0201	0.0917	26.6882	-21.5247	49.3888
9	0.5179	-0.4662	0.6094	7.4878	-1.4868	1.8169	0.0368	-0.0265	-0.2212	0.0766	-0.0908	0.7781	-0.0929	-0.3966	0.054	0.1283	-0.0018	-0.0094	0.153	-0.0463	0.1436	26.1936	-36.5157	47.8376
10	3.8713	-3.4983	0.5267	3.1807	-0.5993	0.8583	0.0167	0.0263	-0.23	0.0365	0.0237	0.1811	0.0363	-0.228	-0.0404	0.0757	-0.0715	0.0025	0.0727	-0.0046	0.1423	26.4653	-39.9595	50.8278
11	3.228	-3.1454	1.3729	4.058	-0.5594	1.1939	0.0639	0.0939	-0.1413	-0.2528	-0.0727	-0.1285	0.0232	-0.0147	0.0088	0.1141	0.0084	-0.0124	0.0968	-0.0203	0.0707	35.7922	-35.0187	40.0813
12	2.0056	-0.8931	-1.2855	3.2976	-0.0994	2.9055	0.0519	-0.1101	-0.0938	0.0536	-0.0011	-0.1772	-0.0067	0.0604	-0.0508	0.0785	0.0104	0.0022	0.0964	0.0078	0.0802	24.9959	-7.8886	57.3296
13	3.8096	1.5679	-1.6739	4.1185	-0.9274	1.1891	-0.0206	0.1055	-0.1088	0.3494	0.0751	0.1286	-0.0621	-0.0054	-0.0545	0.0713	0.0083	-0.0038	0.1094	0.0078	0.0529	22.4853	-11.503	63.6145
14	0.1593	-0.5074	0.3249	1.6157	-1.0346	0.6625	-0.1094	-0.0648	-0.0646	0.1488	0.1463	0.0421	-0.0865	-0.0257	-0.0369	0.0823	0.0249	0.0061	0.1503	-0.0031	0.0887	18.2036	-4.853	60.7166
15	9.0978	1.9423	5.8147	1.5271	4.1205	11.1678	-0.4614	-0.6369	-0.2376	0.1388	0.0769	0.3484	-0.0786	-0.2782	0.3845	0.0914	0.0958	0.0459	0.1505	0.0709	0.0441	10.0618	1.8448	62.5367
16	1.1338	1.096	2.2099	1.7075	1.332	5.3053	0.0698	0.0262	-0.0378	0.158	0.0441	-0.0574	0.2303	0.0115	-0.1139	0.0909	-0.0141	0.0003	0.0928	0.0076	0.0902	16.7303	-0.5047	48.6364
17	5.3802	2.1436	3.111	1.3929	-0.5952	8.0456	-0.1023	-0.3511	0.2648	-0.2642	-0.1629	0.1471	-0.2487	-0.4613	0.2652	0.0768	-0.0094	-0.0093	0.1054	0	0.0731	8.5912	0.5143	39.4864
18	1.1358	-0.9433	0.3378	1.0852	-0.1273	1.0484	-0.0538	0.0349	-0.0356	-0.0825	0.0306	0.0526	-0.0936	0.0071	0.0232	0.0998	-0.0066	0.0038	0.0872	-0.0041	0.1001	16.8605	2.7266	50.0646
19	17.2379	-3.3254	6.865	20.4095	-8.5807	5.3977	-0.0079	0.2822	-0.047	-0.2782	-0.1963	-0.2012	0.5129	0.1285	0.2041	0.0898	0.0387	0.0308	0.1294	0.0053	0.0786	31.1892	-13.0933	48.9475
20	2.8624	0.9294	-2.4931	7.1559	3.2904	5.6134	-0.0231	-0.2529	-0.0761	0.0574	0.083	-0.6516	0.057	0.579	-0.06	0.0996	-0.0591	-0.0102	0.1127	0.0551	0.1226	29.1947	5.4804	48.1584
21	5.4374	-3.0861	0.9153	2.1529	-1.0667	2.064	-0.0064	-0.0058	0.1307	0.0136	-0.0487	-0.1091	-0.1073	0.1935	0.055	0.0899	-0.0536	-0.0057	0.0521	-0.0235	0.0913	30.044	4.1911	48.0417
22	4.0899	-3.7941	-3.4072	3.5197	3.1608	2.8385	-0.0162	0.0471	0.0025	-0.1249	-0.1934	0.1277	-0.0509	-0.0001	0.2095	0.1025	-0.0108	-0.0062	0.111	0.0023	0.0877	20.9314	-0.8653	38.7053

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	29 - 47
2	X-RAY DIFFRACTION	2	A	48 - 66
3	X-RAY DIFFRACTION	3	A	67 - 96
4	X-RAY DIFFRACTION	4	A	97 - 106
5	X-RAY DIFFRACTION	5	A	107 - 120
6	X-RAY DIFFRACTION	6	A	121 - 130
7	X-RAY DIFFRACTION	7	A	131 - 150
8	X-RAY DIFFRACTION	8	A	151 - 155
9	X-RAY DIFFRACTION	9	A	156 - 172
10	X-RAY DIFFRACTION	10	A	173 - 195
11	X-RAY DIFFRACTION	11	A	196 - 208
12	X-RAY DIFFRACTION	12	B	29 - 47
13	X-RAY DIFFRACTION	13	B	48 - 67
14	X-RAY DIFFRACTION	14	B	68 - 96
15	X-RAY DIFFRACTION	15	B	97 - 106
16	X-RAY DIFFRACTION	16	B	107 - 120
17	X-RAY DIFFRACTION	17	B	121 - 128
18	X-RAY DIFFRACTION	18	B	129 - 151
19	X-RAY DIFFRACTION	19	B	152 - 157
20	X-RAY DIFFRACTION	20	B	158 - 176
21	X-RAY DIFFRACTION	21	B	177 - 196
22	X-RAY DIFFRACTION	22	B	197 - 208

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-Structure viewers

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-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

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-Assembly

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-Experimental details

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-Data collection

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+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

-
Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

-
Validation report

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Related structure data

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Links

-
Assembly

-
Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi