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- PDB-3zqs: Human FANCL central domain -

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Basic information

Entry
Database: PDB / ID: 3zqs
TitleHuman FANCL central domain
ComponentsE3 UBIQUITIN-PROTEIN LIGASE FANCL
KeywordsLIGASE
Function / homology
Function and homology information


Fanconi anaemia nuclear complex / gamete generation / protein monoubiquitination / interstrand cross-link repair / Fanconi Anemia Pathway / RING-type E3 ubiquitin transferase / PKR-mediated signaling / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / nuclear envelope ...Fanconi anaemia nuclear complex / gamete generation / protein monoubiquitination / interstrand cross-link repair / Fanconi Anemia Pathway / RING-type E3 ubiquitin transferase / PKR-mediated signaling / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / nuclear envelope / regulation of cell population proliferation / nuclear body / intracellular membrane-bounded organelle / DNA repair / DNA damage response / ubiquitin protein ligase binding / chromatin / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
RWD domain-like / FANCL, UBC-like domain 2 / FANCL, UBC-like domain 3 / Fanconi anemia complex, subunit FancL, WD-repeat containing domain / E3 ubiquitin-protein ligase FANCL / FANCL C-terminal domain / FANCL, UBC-like domain 3 superfamily / FANCL UBC-like domain 1 / FANCL C-terminal domain / FANCL UBC-like domain 2 ...RWD domain-like / FANCL, UBC-like domain 2 / FANCL, UBC-like domain 3 / Fanconi anemia complex, subunit FancL, WD-repeat containing domain / E3 ubiquitin-protein ligase FANCL / FANCL C-terminal domain / FANCL, UBC-like domain 3 superfamily / FANCL UBC-like domain 1 / FANCL C-terminal domain / FANCL UBC-like domain 2 / FANCL UBC-like domain 3 / FANCL C-terminal domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
PROLINE / E3 ubiquitin-protein ligase FANCL
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHodson, C. / Cole, A.R. / Purkiss-Trew, A. / Walden, H.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Analysis of Human Fancl, the E3 Ligase in the Fanconi Anemia Pathway.
Authors: Hodson, C. / Cole, A.R. / Lewis, L.P. / Miles, J.A. / Purkiss-Trew, A. / Walden, H.
History
DepositionJun 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references / Structure summary
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: E3 UBIQUITIN-PROTEIN LIGASE FANCL
B: E3 UBIQUITIN-PROTEIN LIGASE FANCL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,31016
Polymers42,2102
Non-polymers3,10014
Water7,440413
1
A: E3 UBIQUITIN-PROTEIN LIGASE FANCL
B: E3 UBIQUITIN-PROTEIN LIGASE FANCL
hetero molecules

A: E3 UBIQUITIN-PROTEIN LIGASE FANCL
B: E3 UBIQUITIN-PROTEIN LIGASE FANCL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,61932
Polymers84,4204
Non-polymers6,19928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area5960 Å2
ΔGint-65.7 kcal/mol
Surface area37960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.600, 102.520, 65.760
Angle α, β, γ (deg.)90.00, 94.09, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 113:154 OR RESSEQ 162:172 OR RESSEQ...
211CHAIN B AND (RESSEQ 113:154 OR RESSEQ 162:172 OR RESSEQ...

NCS oper: (Code: given
Matrix: (0.359851, 0.270783, 0.892852), (0.225071, -0.953891, 0.198583), (0.905456, 0.129494, -0.404204)
Vector: -48.1818, 4.62347, 71.3414)

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Components

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE FANCL / FANCL / FANCONI ANEMIA GROUP L PROTEIN / FANCONI ANEMIA-ASSOCIATED POLYPEPTIDE OF 43 KDA / FAAP43


Mass: 21105.090 Da / Num. of mol.: 2 / Fragment: URD, RESIDUES 109-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NW38, ubiquitin-protein ligase
#2: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 5.9 Å3/Da / Density % sol: 79 % / Description: NONE
Crystal growpH: 5.5
Details: 0.2M L-PROLINE, 0.1M SODIUM TRI CITRATE PH5.5, 2% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 11, 2009 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→45 Å / Num. obs: 103454 / % possible obs: 79 % / Observed criterion σ(I): 2 / Redundancy: 1.5 % / Biso Wilson estimate: 30.07 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.91
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.03 / % possible all: 75

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K1L, DRWD DOMAIN

3k1l


Resolution: 2→44.265 Å / SU ML: 0.25 / σ(F): 0.96 / Phase error: 24.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2066 5311 5.1 %
Rwork0.1833 --
obs0.1845 103453 79.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.034 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso mean: 41.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.5321 Å20 Å2-5.5817 Å2
2--4.4854 Å20 Å2
3----5.0175 Å2
Refinement stepCycle: LAST / Resolution: 2→44.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 121 413 3504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073287
X-RAY DIFFRACTIONf_angle_d1.1034464
X-RAY DIFFRACTIONf_dihedral_angle_d14.7861271
X-RAY DIFFRACTIONf_chiral_restr0.074495
X-RAY DIFFRACTIONf_plane_restr0.005559
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A785X-RAY DIFFRACTIONPOSITIONAL
12B785X-RAY DIFFRACTIONPOSITIONAL0.077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.34391630.32262992X-RAY DIFFRACTION74
2.0227-2.04650.3281550.31323124X-RAY DIFFRACTION74
2.0465-2.07150.32811470.30172999X-RAY DIFFRACTION74
2.0715-2.09770.29871790.27933060X-RAY DIFFRACTION74
2.0977-2.12530.29411740.27313086X-RAY DIFFRACTION75
2.1253-2.15440.28411530.25443034X-RAY DIFFRACTION75
2.1544-2.18520.26411680.25433094X-RAY DIFFRACTION75
2.1852-2.21780.27771750.25423033X-RAY DIFFRACTION75
2.2178-2.25250.29311360.2433149X-RAY DIFFRACTION75
2.2525-2.28940.24431940.24222976X-RAY DIFFRACTION74
2.2894-2.32890.29591330.22993065X-RAY DIFFRACTION74
2.3289-2.37120.23241450.23313128X-RAY DIFFRACTION75
2.3712-2.41680.25672110.22933055X-RAY DIFFRACTION75
2.4168-2.46610.26451660.22793062X-RAY DIFFRACTION75
2.4661-2.51980.29021670.21683078X-RAY DIFFRACTION75
2.5198-2.57840.22891570.21073106X-RAY DIFFRACTION75
2.5784-2.64280.22221610.19073127X-RAY DIFFRACTION75
2.6428-2.71430.19731650.1933068X-RAY DIFFRACTION75
2.7143-2.79420.2211600.18693040X-RAY DIFFRACTION74
2.7942-2.88430.24631460.18893108X-RAY DIFFRACTION75
2.8843-2.98740.21391720.18753079X-RAY DIFFRACTION75
2.9874-3.1070.19551650.18213055X-RAY DIFFRACTION74
3.107-3.24830.19531550.17883032X-RAY DIFFRACTION74
3.2483-3.41950.21192040.17453684X-RAY DIFFRACTION89
3.4195-3.63370.20732170.17723971X-RAY DIFFRACTION98
3.6337-3.91410.15962180.16094042X-RAY DIFFRACTION98
3.9141-4.30770.17752230.13284024X-RAY DIFFRACTION98
4.3077-4.93030.14362330.12954001X-RAY DIFFRACTION98
4.9303-6.20890.17872340.15043976X-RAY DIFFRACTION98
6.2089-44.27540.18852350.17433894X-RAY DIFFRACTION95
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)
10.22560.032-0.15680.2602-0.09890.1954-0.04670.0593-0.1050.07460.0165-0.0322-0.0151-0.07670.01570.2016-0.00910.00940.1688-0.01360.2042-59.6149-1.59482.6673
20.02020.0446-0.01220.0816-0.01610.03090.02370.0111-0.04470.0548-0.0268-0.029-0.02530.03760.01560.1536-0.1186-0.0690.0287-0.04370.114-41.4657.34194.1187
30.0276-0.0497-0.04730.15270.11690.14040.0988-0.0056-0.10560.0280.0298-0.27680.0230.1717-0.10440.2762-0.08-0.04050.3539-0.10380.4565-21.086314.56388.4818
40.1504-0.03780.0510.18230.13750.56020.0417-0.1751-0.0733-0.07410.01310.0243-0.1071-0.1272-0.01490.21550.0245-0.00050.30290.04270.1878-67.2118-5.521616.0827
50.09450.02980.01960.0596-0.03640.13140.02420.12250.004-0.02380.03970.0383-0.0286-0.1360.04470.11740.18250.0260.31310.02190.1001-58.477-9.352633.8499
60.17250.0685-0.06470.07950.05710.17060.09180.0787-0.00050.03960.0383-0.04160.0030.0512-0.04870.26140.0924-0.00080.2529-0.01790.222-45.1614-10.22752.0797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 109:159)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 160:239)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 240:294)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 109:159)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 160:239)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 240:294)

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