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- PDB-3v5x: Structure of FBXL5 hemerythrin domain, C2 cell -

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Basic information

Entry
Database: PDB / ID: 3v5x
TitleStructure of FBXL5 hemerythrin domain, C2 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 / MAD / Resolution: 1.85 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 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Water2,918162
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)60.118, 75.802, 78.727
Angle α, β, γ (deg.)90.00, 111.75, 90.00
Int Tables number5
Space group name H-MC121

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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.: 162 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 6000, 0.1 M HEPES, 25% ethylene glycol, pH 6.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.98717
SYNCHROTRONAPS 19-BM21.74071, 1.74164
Detector
TypeIDDetectorDateDetails
ADSC Q3151CCDJun 28, 2009monochromator
ADSC Q3152CCDJun 26, 2009monochromator
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHx-ray1
2SAGITALLY FOCUSED Si(111)MADx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.987171
21.740711
31.741641
ReflectionResolution: 1.85→50 Å / Num. obs: 28254 / % possible obs: 99.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.85-1.8850.691,2100
1.88-1.9250.5171,2100
1.92-1.9550.4261,2100
1.95-1.9950.3171,2100
1.99-2.0450.2581,2100
2.04-2.0850.2121,2100
2.08-2.1450.1531,2100
2.14-2.1950.1271,2100
2.19-2.2650.1071,2100
2.26-2.3350.0911,2100
2.33-2.4150.0761,2100
2.41-2.5150.0651,2100
2.51-2.6350.0571,2100
2.63-2.7650.0511,2100
2.76-2.9450.0481,2100
2.94-3.1650.051,2100
3.16-3.484.90.0481,299.7
3.48-3.994.90.0381,2100
3.99-5.024.80.0271,299.9
5.02-504.90.0271,297.4

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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
SHELXDphasing
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→27.682 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.4 / σ(F): 1.34 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2087 1412 5.04 %
Rwork0.1689 --
obs0.1709 28021 99.81 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.344 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.7803 Å2-0 Å25.6076 Å2
2---2.2967 Å2-0 Å2
3----2.4835 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 6 162 2748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122669
X-RAY DIFFRACTIONf_angle_d1.2113574
X-RAY DIFFRACTIONf_dihedral_angle_d14.891030
X-RAY DIFFRACTIONf_chiral_restr0.073370
X-RAY DIFFRACTIONf_plane_restr0.006460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.91610.28971340.21922677X-RAY DIFFRACTION100
1.9161-1.99280.22961510.18182634X-RAY DIFFRACTION100
1.9928-2.08350.21471390.17122637X-RAY DIFFRACTION100
2.0835-2.19330.20421580.15362645X-RAY DIFFRACTION100
2.1933-2.33060.22291250.15682676X-RAY DIFFRACTION100
2.3306-2.51050.19331190.16612675X-RAY DIFFRACTION100
2.5105-2.76290.21991500.16322639X-RAY DIFFRACTION100
2.7629-3.16220.18081350.17692693X-RAY DIFFRACTION100
3.1622-3.98220.20111570.16372658X-RAY DIFFRACTION100
3.9822-27.68530.21491440.17052675X-RAY DIFFRACTION99
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)
13.4532-1.9901-1.8515.36252.1184.01490.0927-0.20.08990.0748-0.019-0.10340.08620.0746-0.08810.178-0.03240.01350.18540.04540.15151.6579-15.289729.7886
23.4722.53390.55153.2032-1.25842.1238-0.02640.40160.8464-0.78390.1974-0.3724-0.69270.2481-0.29780.7249-0.07760.10720.36740.14090.6671-0.67433.210425.2201
33.7559-2.6836-2.2425.79114.45095.88160.16490.4238-0.1987-0.7491-0.37770.2229-0.5565-0.46030.22920.3420.0614-0.00010.33810.03020.26141.5378-21.394113.2973
42.2776-2.8478-3.28925.16056.24828.20450.2506-0.21220.3297-0.41680.2782-0.5485-0.45940.7068-0.48430.3013-0.01140.08280.3490.01720.318710.3301-15.289120.2713
54.773-1.6483-2.45912.4532.36473.09190.1232-0.38090.8445-0.75360.2431-0.0414-0.97820.4571-0.16460.5649-0.1780.14190.3515-0.15390.519-1.22424.825140.0913
62.14751.31750.50646.91183.93185.20590.2866-0.31920.17211.0938-0.31420.53340.3325-0.22160.01630.3512-0.08390.08720.2887-0.02330.2594-8.7681-6.582942.3367
72.0235-0.7525-1.04115.83144.40986.27660.0010.1271-0.06850.0807-0.0384-0.00290.07480.06050.01840.142-0.0076-0.01190.14620.03710.135111.24554.39365.6119
80.656-0.48340.14582.7798-2.07931.6371-0.21540.0629-0.34931.5979-0.17460.19291.4856-0.1010.52420.9578-0.130.220.31210.04680.66775.8975-13.54787.4248
91.4975-1.7582-1.54075.32364.59186.1697-0.1638-0.1212-0.2830.7901-0.09230.33850.93030.07830.20720.3182-0.02190.02530.17060.0230.21078.85522.522814.7884
104.6776-3.1208-2.29652.95871.85456.8090.33970.4032-0.1886-1.3555-0.30070.023-0.38570.0611-0.02960.3080.0723-0.00560.2379-0.00270.221712.4081-5.2135-10.8545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:73)
2X-RAY DIFFRACTION2chain 'A' and (resseq 74:84)
3X-RAY DIFFRACTION3chain 'A' and (resseq 85:101)
4X-RAY DIFFRACTION4chain 'A' and (resseq 102:132)
5X-RAY DIFFRACTION5chain 'A' and (resseq 133:143)
6X-RAY DIFFRACTION6chain 'A' and (resseq 144:159)
7X-RAY DIFFRACTION7chain 'B' and (resseq 4:73)
8X-RAY DIFFRACTION8chain 'B' and (resseq 74:84)
9X-RAY DIFFRACTION9chain 'B' and (resseq 85:141)
10X-RAY DIFFRACTION10chain 'B' and (resseq 142:160)

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