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- PDB-3u9m: Structure of reduced human FBXL5 hemerythrin like domain -

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Basic information

Entry
Database: PDB / ID: 3u9m
TitleStructure of reduced human FBXL5 hemerythrin like domain
ComponentsF-box/LRR-repeat protein 5
KeywordsPROTEIN BINDING / F-box / LRR / E3 / Iron sensor
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 / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / 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 / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / 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 / A Receptor for Ubiquitination Targets / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box domain profile. / F-box-like / F-box-like domain superfamily ...nmb1532 protein domain like / FBXL5-like, hemerythrin-like domain / Hemerythrin-like / Hemerythrin HHE cation binding domain / A Receptor for Ubiquitination Targets / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box domain profile. / F-box-like / F-box-like domain superfamily / 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
: / F-box/LRR-repeat protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLi, P.
CitationJournal: Chembiochem / Year: 2012
Title: The Structural Basis of Iron Sensing by the Human F-box Protein FBXL5.
Authors: Shu, C. / Sung, M.W. / Stewart, M.D. / Igumenova, T.I. / Tan, X. / Li, P.
History
DepositionOct 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Feb 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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
C: F-box/LRR-repeat protein 5
E: F-box/LRR-repeat protein 5
G: F-box/LRR-repeat protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,36712
Polymers76,9204
Non-polymers4478
Water5,332296
1
A: F-box/LRR-repeat protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3423
Polymers19,2301
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: F-box/LRR-repeat protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3423
Polymers19,2301
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: F-box/LRR-repeat protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3423
Polymers19,2301
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: F-box/LRR-repeat protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3423
Polymers19,2301
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.086, 77.538, 73.641
Angle α, β, γ (deg.)90.00, 110.55, 90.00
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: 19230.006 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXL5, FBL4, FBL5, FLR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKA1
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.02 Å3/Da / Density % sol: 39.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 31, 2011 / Details: Osmic
RadiationMonochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→29 Å / Num. all: 44730 / Num. obs: 43657 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.95→2.02 Å / % possible all: 90.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 29.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1927 4.6 %Random
Rwork0.2036 ---
all0.206 44730 --
obs0.2056 41903 93.34 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.056 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.4858 Å20 Å2-14.4412 Å2
2---9.7427 Å2-0 Å2
3---3.2568 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5320 0 8 296 5624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045436
X-RAY DIFFRACTIONf_angle_d0.8227296
X-RAY DIFFRACTIONf_dihedral_angle_d13.8972092
X-RAY DIFFRACTIONf_chiral_restr0.069764
X-RAY DIFFRACTIONf_plane_restr0.003940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9467-1.99530.316980.26622145X-RAY DIFFRACTION70
1.9953-2.04930.34621220.26172662X-RAY DIFFRACTION88
2.0493-2.10960.31271390.24122734X-RAY DIFFRACTION90
2.1096-2.17760.28111440.21822846X-RAY DIFFRACTION94
2.1776-2.25540.25991270.222882X-RAY DIFFRACTION94
2.2554-2.34570.26631370.21012872X-RAY DIFFRACTION95
2.3457-2.45240.27851430.21072948X-RAY DIFFRACTION96
2.4524-2.58160.28261400.21142945X-RAY DIFFRACTION97
2.5816-2.74320.30071520.21222973X-RAY DIFFRACTION97
2.7432-2.95490.27131400.21813009X-RAY DIFFRACTION98
2.9549-3.25190.26151580.2163017X-RAY DIFFRACTION98
3.2519-3.72160.23621410.18662977X-RAY DIFFRACTION97
3.7216-4.68560.20271480.172942X-RAY DIFFRACTION96
4.6856-29.0150.21331380.20763024X-RAY DIFFRACTION96
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)
10.46760.33290.43721.09010.15740.7918-0.1280.08190.0855-0.20790.05180.0534-0.20570.06390.02510.2330.01920.02920.2770.01680.2677-26.20715.6346.6091
22.5594-0.88340.16940.4547-0.45671.0893-0.2339-0.8395-0.83770.47010.5740.38360.37770.0733-0.25510.5027-0.01950.04140.33740.09210.4149-37.8156-16.79013.4516
32.290.1555-2.24841.45220.38392.55870.5943-0.45820.05030.12760.26620.0026-0.13090.28150.76670.4471-0.1269-0.22280.26460.15080.3678-29.7553-14.792610.6919
40.76030.59080.3321.5890.85570.59880.17380.005-0.17610.29070.0194-0.19210.3510.1276-0.06640.33120.0077-0.02130.30170.01190.3158-26.4884-0.96769.2156
50.4121-0.25230.41331.378-0.04580.90170.0428-0.126-0.0114-0.0102-0.14420.003-0.0556-0.17780.0580.26630.05310.02170.3237-0.02280.2579-17.6884-17.642329.478
60.13760.01960.06560.13450.06010.41580.4165-0.1383-0.0283-0.06830.00060.00880.25630.20920.53831.26810.2667-0.4990.55750.3558-0.0841-20.27810.215426.8893
70.27310.44080.25992.09250.53061.071-0.170.11290.1247-0.5163-0.02330.1888-0.48710.13530.09740.34840.0498-0.02840.3318-0.02810.291-18.6793-14.181926.2977
80.95050.02440.64481.02870.5571.0838-0.0109-0.0620.1761-0.11530.0262-0.09360.0806-0.0166-0.00390.1930.0030.05580.28-0.02340.2673-0.82945.3484-6.8788
90.31390.0954-0.23140.30860.31120.7152-0.1433-0.17580.1139-0.2554-0.5039-0.01970.3335-0.43980.14010.6982-0.06710.01570.5404-0.16460.6436-1.0097-12.4103-10.3484
100.4295-0.25320.3791.3889-0.44480.99040.1642-0.092-0.1832-0.16170.07340.31690.183-0.3205-0.1040.1901-0.0187-0.01740.26590.01910.3132-2.87761.8527-9.5572
110.5965-0.64941.12192.0791-1.10071.25610.23010.2242-0.0857-0.7345-0.10660.46890.56720.3493-0.06380.35780.0127-0.04430.36930.05350.3294-38.4993-15.358539.8828
120.5508-0.05420.21740.17240.0630.11880.1526-0.1475-0.512-0.15860.0463-0.06880.03410.12220.02620.8492-0.0723-0.40110.423-0.12250.7465-34.34933.401940.5903
13-0.2020.14790.44372.7472-1.52561.2358-0.0310.08140.05030.3496-0.16220.0561-0.55510.31250.04630.37240.04290.03050.38280.04120.3322-36.9243-11.286942.5145
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:64)
2X-RAY DIFFRACTION2chain 'A' and (resseq 65:73)
3X-RAY DIFFRACTION3chain 'A' and (resseq 74:84)
4X-RAY DIFFRACTION4chain 'A' and (resseq 85:160)
5X-RAY DIFFRACTION5chain 'C' and (resseq 4:73)
6X-RAY DIFFRACTION6chain 'C' and (resseq 74:84)
7X-RAY DIFFRACTION7chain 'C' and (resseq 85:160)
8X-RAY DIFFRACTION8chain 'E' and (resseq 4:73)
9X-RAY DIFFRACTION9chain 'E' and (resseq 74:84)
10X-RAY DIFFRACTION10chain 'E' and (resseq 85:160)
11X-RAY DIFFRACTION11chain 'G' and (resseq 4:72)
12X-RAY DIFFRACTION12chain 'G' and (resseq 73:84)
13X-RAY DIFFRACTION13chain 'G' and (resseq 85:160)

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