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- PDB-3v5z: Structure of FBXL5 hemerythrin domain, C2 cell, grown anaerobically -

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Basic information

Entry
Database: PDB / ID: 3v5z
TitleStructure of FBXL5 hemerythrin domain, C2 cell, grown anaerobically
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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Leucine-rich repeat / 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: 2.1847 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9724
Polymers38,7162
Non-polymers2552
Water82946
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
Unit cell
Length a, b, c (Å)60.442, 76.051, 77.433
Angle α, β, γ (deg.)90.000, 112.120, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

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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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Fe2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 6000, 0.1 M HEPES, 30% ethylene glycol, 2M Na(2)S(2)O(4), pH 6.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC Q315 / Detector: CCD / Date: Jun 19, 2010 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.184→50 Å / Num. obs: 16703 / % possible obs: 99.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.062 / Χ2: 1.207 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.184-2.243.70.5528491.1281100
2.24-2.283.90.4238011.061100
2.28-2.3240.3598601.0651100
2.32-2.374.10.3268001.0541100
2.37-2.424.10.2788551.0731100
2.42-2.484.20.2268261.1571100
2.48-2.544.10.218561.2281100
2.54-2.614.10.1728131.246199.9
2.61-2.694.10.1498351.3581100
2.69-2.774.10.1238271.4041100
2.77-2.874.10.1078691.1591100
2.87-2.994.10.0898001.2511100
2.99-3.124.10.0868411.4199.9
3.12-3.2940.0688451.261100
3.29-3.493.90.0568331.246199.9
3.49-3.763.90.0518431.177199.9
3.76-4.143.80.0498351.236199.8
4.14-4.743.70.058371.138199.4
4.74-5.973.70.0468491.302199.8
5.97-503.60.0398291.181195

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
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: 2.1847→33.83 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.53 / σ(F): 0 / Phase error: 23.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 816 4.89 %RANDOM
Rwork0.1771 ---
obs0.1794 16694 98.76 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.64 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso max: 143.49 Å2 / Biso mean: 59.5433 Å2 / Biso min: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.3038 Å20 Å2-9.7158 Å2
2---2.3177 Å2-0 Å2
3----2.9861 Å2
Refinement stepCycle: LAST / Resolution: 2.1847→33.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2626 0 6 46 2678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082724
X-RAY DIFFRACTIONf_angle_d1.0123656
X-RAY DIFFRACTIONf_chiral_restr0.076381
X-RAY DIFFRACTIONf_plane_restr0.004473
X-RAY DIFFRACTIONf_dihedral_angle_d15.6361050
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1847-2.32150.32461090.23932542265195
2.3215-2.50070.25451200.20326522772100
2.5007-2.75230.23571480.191326692817100
2.7523-3.15030.26151400.177926642804100
3.1503-3.9680.21581510.168426752826100
3.968-33.83430.19961480.16722676282498
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)
14.036-1.1622.84145.1141-0.61114.3498-0.2231-0.96760.07371.09830.35450.1834-0.4644-0.8759-0.15580.4201-0.00440.08550.48460.0230.3572-4.223914.500335.4514
21.891-1.40891.50415.0858-1.04564.25090.01920.09380.1579-0.1495-0.11740.0192-0.44650.05920.1020.4556-0.0285-0.02680.3701-0.03990.4487-0.263320.392623.2132
33.49960.2286-0.24633.62580.51632.03580.81461.2797-1.8991-1.27110.10450.16571.5260.0525-1.11530.88890.0119-0.26110.599-0.1820.88784.9114-4.160728.3156
44.66321.7088-1.37552.7266-4.1697.3484-0.4450.674-0.1839-1.67410.3138-0.22220.450.04860.03960.5849-0.0058-0.0160.5658-0.07790.4001-0.366319.689713.7641
52.8722-2.10691.47344.67-2.80645.1344-0.09490.1057-0.5877-0.1290.3656-0.0278-0.3088-0.4615-0.27250.59980.1314-0.11010.5508-0.03530.5362-11.007425.20219.8993
63.0154-1.18861.9295.9482-4.29017.23890.2802-0.4604-0.6519-0.36070.46971.17090.4338-1.4502-0.64920.4317-0.0881-0.1010.64810.03280.6052-8.1117.816927.0805
76.4934-1.45274.0881.894-1.79813.02580.7518-0.9308-1.7994-0.16550.30210.37991.3196-0.617-0.96710.7199-0.2101-0.21950.51080.15610.68512.3823-5.223139.1355
83.50291.2018-0.79482.6676-3.18254.59030.1855-0.2148-0.55741.5763-0.0035-0.7542-0.3913-0.0034-0.03830.6517-0.061-0.110.45450.0270.52279.82846.300441.4445
91.5303-0.09690.94986.5876-4.58977.4955-0.0062-0.0447-0.0876-0.33230.79550.98650.3716-1.3068-0.61530.2475-0.00120.04670.45470.03830.4317-18.1119-4.07223.6907
102.3159-1.12032.1226.6994-3.13715.73540.05370.0859-0.0742-0.1376-0.3054-0.46620.43410.05880.32640.29960.02010.02580.3402-0.02230.3597-6.7611-8.9548.5474
110.7036-1.60581.17063.7156-2.77532.0915-0.4459-0.43750.65152.8031-0.2825-1.2526-2.85071.19510.89891.1971-0.256-0.13330.52560.0440.6826-5.883713.7542.7119
125.9118-5.38670.3677.0843-1.04475.6272-0.7075-0.28290.94660.80070.8324-1.9942-0.20660.80250.10.3988-0.0617-0.07860.47260.00710.64270.5846-10.235616.0674
134.3267-2.10182.93798.1836-5.87196.6222-0.2027-0.60970.78850.3236-0.0693-1.1105-0.2773-0.36210.22090.5781-0.0533-0.00220.47370.0080.4171-4.2418-14.86526.2231
144.5696-3.4013.64359.0488-5.48158.0988-0.4359-0.22150.52780.97550.3296-0.404-1.2441-0.6924-0.1610.38480.08630.06640.4709-0.00070.3943-14.17522.188912.6122
151.8053-0.43720.10133.7809-0.99999.37940.3949-0.05560.42120.21730.30050.7218-1.5145-0.603-0.29680.59620.15380.1020.4260.02460.6009-16.447714.752-4.2855
163.8913-1.80890.40413.3794-3.68695.8240.26860.25060.3911-2.6558-0.3789-0.42920.8417-0.10610.10710.71670.11-0.00310.4850.02290.3631-11.78352.5091-10.4292
175.32822.88552.64854.9023-0.52092.77094.01855.4137-1.2798-13.3895-11.99495.1284-25.7092-26.38768.09430.5312-0.01080.05540.59640.01950.5793-0.12966.422730.3903
182.49532.25972.25552.04662.04252.038617.4672-21.3794-23.23419.7803-8.5772-12.1288.5659-12.4331-9.03670.48610.0094-0.06290.49190.06310.7074-11.45723.87364.1156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:31)A4 - 31
2X-RAY DIFFRACTION2(chain A and resid 32:64)A32 - 64
3X-RAY DIFFRACTION3(chain A and resid 65:84)A65 - 84
4X-RAY DIFFRACTION4(chain A and resid 85:99)A85 - 99
5X-RAY DIFFRACTION5(chain A and resid 100:114)A100 - 114
6X-RAY DIFFRACTION6(chain A and resid 115:132)A115 - 132
7X-RAY DIFFRACTION7(chain A and resid 133:143)A133 - 143
8X-RAY DIFFRACTION8(chain A and resid 144:159)A144 - 159
9X-RAY DIFFRACTION9(chain B and resid 4:31)B4 - 31
10X-RAY DIFFRACTION10(chain B and resid 32:67)B32 - 67
11X-RAY DIFFRACTION11(chain B and resid 68:85)B68 - 85
12X-RAY DIFFRACTION12(chain B and resid 86:99)B86 - 99
13X-RAY DIFFRACTION13(chain B and resid 100:114)B100 - 114
14X-RAY DIFFRACTION14(chain B and resid 115:131)B115 - 131
15X-RAY DIFFRACTION15(chain B and resid 132:144)B132 - 144
16X-RAY DIFFRACTION16(chain B and resid 145:160)B145 - 160
17X-RAY DIFFRACTION17(chain A and resid 201)A201
18X-RAY DIFFRACTION18(chain B and resid 201)B201

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