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- PDB-3v5y: Structure of FBXL5 hemerythrin domain, P2(1) cell -

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Basic information

Entry
Database: PDB / ID: 3v5y
TitleStructure of FBXL5 hemerythrin domain, P2(1) cell
ComponentsF-box/LRR-repeat protein 5
KeywordsGENE REGULATION / hemerythrin / alpha helical bundle / E3 ubiquitin ligase complex
Function / homology
Function and homology information


SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Association of TriC/CCT with target proteins during biosynthesis / ubiquitin ligase complex / Iron uptake and transport / 2 iron, 2 sulfur cluster binding / multicellular organismal-level iron ion homeostasis / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation ...SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Association of TriC/CCT with target proteins during biosynthesis / ubiquitin ligase complex / Iron uptake and transport / 2 iron, 2 sulfur cluster binding / multicellular organismal-level iron ion homeostasis / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / intracellular iron ion homeostasis / protein ubiquitination / iron ion binding / perinuclear region of cytoplasm / nucleus / cytosol
Similarity search - Function
nmb1532 protein domain like / FBXL5-like, hemerythrin-like domain / Hemerythrin-like / Hemerythrin HHE cation binding domain / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like ...nmb1532 protein domain like / FBXL5-like, hemerythrin-like domain / Hemerythrin-like / Hemerythrin HHE cation binding domain / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / F-box domain / Leucine Rich repeat / Leucine-rich repeat / Four Helix Bundle (Hemerythrin (Met), subunit A) / Leucine-rich repeat domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
MU-OXO-DIIRON / F-box/LRR-repeat protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTomchick, D.R. / Bruick, R.K. / Thompson, J.W. / Brautigam, C.A.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Structural and Molecular Characterization of Iron-sensing Hemerythrin-like Domain within F-box and Leucine-rich Repeat Protein 5 (FBXL5).
Authors: Thompson, J.W. / Salahudeen, A.A. / Chollangi, S. / Ruiz, J.C. / Brautigam, C.A. / Makris, T.M. / Lipscomb, J.D. / Tomchick, D.R. / Bruick, R.K.
#1: Journal: Science / Year: 2009
Title: An E3 ligase possessing an iron-responsive hemerythrin domain is a regulator of iron homeostasis.
Authors: Salahudeen, A.A. / Thompson, J.W. / Ruiz, J.C. / Ma, H.W. / Kinch, L.N. / Li, Q. / Grishin, N.V. / Bruick, R.K.
History
DepositionDec 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-box/LRR-repeat protein 5
B: F-box/LRR-repeat protein 5
C: F-box/LRR-repeat protein 5
D: F-box/LRR-repeat protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9438
Polymers77,4334
Non-polymers5114
Water4,504250
1
A: F-box/LRR-repeat protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4862
Polymers19,3581
Non-polymers1281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: F-box/LRR-repeat protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4862
Polymers19,3581
Non-polymers1281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: F-box/LRR-repeat protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4862
Polymers19,3581
Non-polymers1281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: F-box/LRR-repeat protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4862
Polymers19,3581
Non-polymers1281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.257, 54.373, 78.215
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
F-box/LRR-repeat protein 5 / F-box and leucine-rich repeat protein 5 / F-box protein FBL4/FBL5 / p45SKP2-like protein


Mass: 19358.135 Da / Num. of mol.: 4 / Fragment: Hemerythrin domain (UNP Residues 1-161)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBL4, FBL5, FBXL5, FLR1 / Plasmid: pGST-parallel / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UKA1
#2: Chemical
ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 25% PEG 3350, 0.1 M HEPES, 20% ethylene glycol, pH 7.4, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97188 Å
DetectorType: ADSC Q315 / Detector: CCD / Date: Aug 6, 2009 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97188 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 37291 / % possible obs: 97.5 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.063 / Χ2: 1.15 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.142.50.59718451.036198.8
2.14-2.182.60.50218971.054198.9
2.18-2.222.60.46318731.07198.9
2.22-2.262.60.39918611.265198.4
2.26-2.312.60.38618901.241198.5
2.31-2.372.70.30318491.146198.6
2.37-2.422.70.27118771.123198.5
2.42-2.492.70.23718951.176198.6
2.49-2.562.70.18918381.109198
2.56-2.652.70.17218861.141198.1
2.65-2.742.70.13718851.173198.1
2.74-2.852.70.11318551.151197.9
2.85-2.982.70.08318631.141197.7
2.98-3.142.70.07618691.166197.3
3.14-3.332.80.05718421.108197.2
3.33-3.592.80.03918711.09196.9
3.59-3.952.80.03418571.269196.2
3.95-4.522.80.02818501.201196.1
4.52-5.72.80.02718401.105195.1
5.7-502.70.02818481.213191.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V5X

3v5x


Resolution: 2.1→29.307 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.64 / σ(F): 1.34 / Phase error: 34.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2698 1832 5 %RANDOM
Rwork0.1971 ---
obs0.2009 36671 97.26 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.023 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso max: 150.48 Å2 / Biso mean: 47.737 Å2 / Biso min: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.1156 Å20 Å2-0.6795 Å2
2--13.59 Å20 Å2
3----9.4744 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5107 0 12 250 5369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0175269
X-RAY DIFFRACTIONf_angle_d1.4037099
X-RAY DIFFRACTIONf_chiral_restr0.076732
X-RAY DIFFRACTIONf_plane_restr0.006892
X-RAY DIFFRACTIONf_dihedral_angle_d16.6332017
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.15680.34291180.25252690280898
2.1568-2.22020.29211440.26122715285999
2.2202-2.29180.35561480.25772658280698
2.2918-2.37370.35791370.22932739287699
2.3737-2.46870.24851350.20322664279998
2.4687-2.5810.28621310.19872697282898
2.581-2.7170.32911340.19672727286198
2.717-2.88710.32531330.20012684281798
2.8871-3.10980.28561430.19742664280797
3.1098-3.42230.26081440.19222677282197
3.4223-3.91650.25991550.17612662281796
3.9165-4.93060.22041330.16282662279595
4.9306-29.30960.23921770.2032600277792
Refinement TLS params.

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

IDL11 (°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)
14.48270.0361-2.450.8735-0.20564.83590.0921-0.07850.06690.1480.07150.0156-0.002-0.0696-0.17520.2237-0.0648-0.05590.09820.03970.220629.244812.73397.029
21.7247-3.18050.15085.9086-0.3241.06170.1951-0.4657-1.04360.03281.33970.5968-0.2462-1.057-0.92090.258-0.0573-0.08721.1350.09020.57868.96168.46694.8556
33.07911.4357-3.94642.072-0.30456.9627-0.6590.7061-0.6201-0.2839-0.1863-0.0750.6618-0.97450.59170.4237-0.10530.03330.1531-0.01460.285234.14686.9788-7.7763
44.1968-0.3057-4.10520.6675-0.09877.01530.16520.54960.0333-0.153600.2341-0.5211-0.7772-0.21160.3435-0.0412-0.02820.21570.05720.281728.682717.577-4.3392
53.99861.07-3.34730.9526-0.23326.9293-0.0405-0.36290.13190.13490.09750.2966-0.0535-0.5279-0.03910.29750.00220.02210.28720.00250.243315.126510.639720.9498
64.6904-0.5078-2.3930.8887-0.1644.2426-0.1766-0.1712-0.0249-0.123-0.01270.0462-0.0059-0.1520.18660.2142-0.065-0.02180.2677-0.00840.1926.204913.5405-17.261
72.5285-2.10460.52763.01370.06770.3378-0.1688-1.19420.930.41330.2114-0.88-0.22321.5368-0.36640.36050.0320.04970.81080.06790.391927.92626.2799-22.0785
81.7691-2.2252-1.61433.50561.39465.6109-0.2735-0.8226-0.53150.2577-0.1044-0.25210.5760.44340.06920.35130.07760.00370.57540.16940.36184.03016.7469-3.5263
93.4839-0.1453-2.07110.9473-0.13542.0429-0.0086-0.47140.1507-0.03980.086-0.086-0.39650.7108-0.06720.2281-0.1108-0.02980.3088-0.03470.213615.644414.1899-18.4656
105.21880.50983.19771.08480.78455.21320.0677-0.1587-0.0760.11810.03380.06310.0468-0.0552-0.10820.207-0.04720.03350.0909-0.00820.183244.258114.45-33.0634
115.22760.16441.50863.3032-0.56340.74470.10621.75350.4181-0.09660.293-0.63710.33591.15640.00280.3108-0.19760.11140.8429-0.00110.435966.199921.0874-29.5128
122.7181.2872.63933.1201-0.46046.7785-0.68170.68380.8159-0.2637-0.10470.1519-0.77290.74730.53280.3768-0.1202-0.02960.20410.05520.297442.113421.2384-46.7311
133.21350.93183.24680.91881.11014.95740.10660.5645-0.2317-0.04510.1242-0.16330.60531.0999-0.17840.3344-0.00620.01540.2666-0.09280.265752.066711.0804-38.692
144.4465-0.92095.65031.4901-0.80567.8318-0.2645-1.1437-0.13260.1940.3761-0.09760.3367-0.2075-0.02290.27790.0030.00690.32260.01030.253857.813119.7756-15.9378
153.72261.03992.69321.31421.66514.68890.567-0.7691-0.57530.5466-0.28920.02070.9013-0.8344-0.24230.2985-0.0194-0.03140.28010.0630.28749.0306-17.2857-16.6195
164.5620.85082.08251.4234-0.194.8201-0.30230.48110.2744-0.03860.03770.057-0.23450.31080.27080.17960.06550.0130.22980.02230.20358.4669-8.1261-23.6598
174.90541.182-0.67571.1381-0.45181.28810.03321.1191-0.6237-0.24950.4826-0.91230.16150.0878-0.18630.2780.11760.28481.0407-0.44260.72827.0354-8.4598-24.2151
185.60630.71774.37260.6560.76224.5211-0.02641.069-0.0446-0.05870.0895-0.0780.20911.0335-0.03360.28150.05050.05090.4472-0.03190.225210.9993-12.9968-29.8395
196.3171-0.14623.13861.6837-0.6373.6199-0.2563-0.99570.36080.25660.0260.0748-0.2689-0.1130.33490.28120.1145-0.00020.3002-0.04390.256419.002-7.0767-4.9321
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 5:73)A5 - 73
2X-RAY DIFFRACTION2chain A and (resseq 74:83)A74 - 83
3X-RAY DIFFRACTION3chain A and (resseq 84:101)A84 - 101
4X-RAY DIFFRACTION4chain A and (resseq 102:132)A102 - 132
5X-RAY DIFFRACTION5chain A and (resseq 133:159)A133 - 159
6X-RAY DIFFRACTION6chain B and (resseq 5:64)B5 - 64
7X-RAY DIFFRACTION7chain B and (resseq 65:83)B65 - 83
8X-RAY DIFFRACTION8chain B and (resseq 84:101)B84 - 101
9X-RAY DIFFRACTION9chain B and (resseq 102:159)B102 - 159
10X-RAY DIFFRACTION10chain C and (resseq 5:64)C5 - 64
11X-RAY DIFFRACTION11chain C and (resseq 65:83)C65 - 83
12X-RAY DIFFRACTION12chain C and (resseq 84:101)C84 - 101
13X-RAY DIFFRACTION13chain C and (resseq 102:141)C102 - 141
14X-RAY DIFFRACTION14chain C and (resseq 142:159)C142 - 159
15X-RAY DIFFRACTION15chain D and (resseq 5:31)D5 - 31
16X-RAY DIFFRACTION16chain D and (resseq 32:72)D32 - 72
17X-RAY DIFFRACTION17chain D and (resseq 73:84)D73 - 84
18X-RAY DIFFRACTION18chain D and (resseq 85:141)D85 - 141
19X-RAY DIFFRACTION19chain D and (resseq 142:160)D142 - 160

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