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- PDB-4ccg: Structure of an E2-E3 complex -

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Basic information

Entry
Database: PDB / ID: 4ccg
TitleStructure of an E2-E3 complex
Components
  • E3 UBIQUITIN-PROTEIN LIGASE FANCL
  • UBIQUITIN-CONJUGATING ENZYME E2 T
KeywordsLIGASE
Function / homology
Function and homology information


Fanconi anaemia nuclear complex / protein K29-linked ubiquitination / protein K27-linked ubiquitination / gamete generation / protein K6-linked ubiquitination / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination ...Fanconi anaemia nuclear complex / protein K29-linked ubiquitination / protein K27-linked ubiquitination / gamete generation / protein K6-linked ubiquitination / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination / interstrand cross-link repair / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Fanconi Anemia Pathway / RING-type E3 ubiquitin transferase / PKR-mediated signaling / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / nuclear envelope / regulation of cell population proliferation / nuclear body / intracellular membrane-bounded organelle / DNA repair / ubiquitin protein ligase binding / DNA damage response / chromatin binding / chromatin / nucleolus / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
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, 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, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
AMMONIUM ION / Ubiquitin-conjugating enzyme E2 T / E3 ubiquitin-protein ligase FANCL
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHodson, C. / Purkiss, A. / Walden, H.
CitationJournal: Structure / Year: 2014
Title: Structure of the Human Fancl Ring-Ube2T Complex Reveals Determinants of Cognate E3-E2 Selection.
Authors: Hodson, C. / Purkiss, A. / Miles, J.A. / Walden, H.
History
DepositionOct 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Feb 19, 2014Group: 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_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: UBIQUITIN-CONJUGATING ENZYME E2 T
B: UBIQUITIN-CONJUGATING ENZYME E2 T
X: E3 UBIQUITIN-PROTEIN LIGASE FANCL
Y: E3 UBIQUITIN-PROTEIN LIGASE FANCL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,55319
Polymers68,1784
Non-polymers1,37515
Water2,054114
1
B: UBIQUITIN-CONJUGATING ENZYME E2 T
Y: E3 UBIQUITIN-PROTEIN LIGASE FANCL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4668
Polymers34,0892
Non-polymers3776
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-43.9 kcal/mol
Surface area11220 Å2
MethodPISA
2
A: UBIQUITIN-CONJUGATING ENZYME E2 T
X: E3 UBIQUITIN-PROTEIN LIGASE FANCL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,08711
Polymers34,0892
Non-polymers9989
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-24.7 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.224, 109.224, 117.728
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.1878, 0.7446, -0.6406), (-0.8187, 0.479, 0.3168), (0.5427, 0.465, 0.6995)-40.35, 72.3, -28.89
2given(0.2178, 0.7261, -0.6521), (-0.8002, 0.5154, 0.3067), (0.5588, 0.455, 0.6933)-40.07, 69.14, -28.81

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Components

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Protein , 2 types, 4 molecules ABXY

#1: Protein UBIQUITIN-CONJUGATING ENZYME E2 T / CELL PROLIFERATION-INDUCING GENE 50 PROTEIN / UBIQUITIN CARRIER PROTEIN T / UBIQUITIN-PROTEIN ...CELL PROLIFERATION-INDUCING GENE 50 PROTEIN / UBIQUITIN CARRIER PROTEIN T / UBIQUITIN-PROTEIN LIGASE T / FANCL RING E3 LIGASE AND UBE2T


Mass: 24008.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RING DOMAIN OF FANCL FUSED BY LINKER TO N-TERMINAL OF UBE2T TO GENERATE A FUSION POLYPEPTIDE.
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: CHAMPION PET SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NPD8
#2: Protein E3 UBIQUITIN-PROTEIN LIGASE FANCL / FANCONI ANEMIA GROUP L PROTEIN / FANCONI ANEMIA-ASSOCIATED POLYPEPTIDE OF 43 KDA / FAAP43 / FANCL ...FANCONI ANEMIA GROUP L PROTEIN / FANCONI ANEMIA-ASSOCIATED POLYPEPTIDE OF 43 KDA / FAAP43 / FANCL RING E3 LIGASE AND UBE2T


Mass: 10080.586 Da / Num. of mol.: 2 / Fragment: RING DOMAIN OF FANCL, RESIDUES 288-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: CHAMPION PET SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NW38, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Non-polymers , 8 types, 129 molecules

#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE FOR UBE2T. IT HAS THE RING DOMAIN FROM UNIPROT Q9NW38 FUSED TO THE N-TERMINUS OF UBE2T ...SEQUENCE FOR UBE2T. IT HAS THE RING DOMAIN FROM UNIPROT Q9NW38 FUSED TO THE N-TERMINUS OF UBE2T SEQUENCE CHAIN A AND B ARE OF UBE2T AND CHAIN X AND Y ARE OF THE RING DOMAIN OF FANCL. THE RECOMBINANT PROTEIN WAS DESIGNED AS THE RING DOMAIN FROM B FANCL - FOLLOWED BY A LINKER - THEN UBE2T. IT IS UNCLEAR FROM THE DENSITY WHETHER THE COMPLEX (CHAIN A AND X OR CHAIN B AND Y, AS THE DESIGNED RECOMBINANT PROTEIN) ARE FROM THE SAME POLYPEPTIDE CHAIN AS NO ELECTRON DENSITY IS VISIBLE FOR EITHER OF THE LINKER REGIONS IN THE ASUS.

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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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 7.5
Details: 1.6M AMMOMIUM SULPHATE, 0.1M HEPES PH7.5, 0.2M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96864
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2013 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96864 Å / Relative weight: 1
ReflectionResolution: 2.4→46.82 Å / Num. obs: 28506 / % possible obs: 100 % / Observed criterion σ(I): 1.2 / Redundancy: 6.8 % / Biso Wilson estimate: 63.41 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1YH2, 3K1L

1yh2

3k1l


Resolution: 2.4→46.817 Å / SU ML: 0.37 / σ(F): 1.33 / Phase error: 30.48 / Stereochemistry target values: ML / Details: THE 14 LINKER RESIDUES ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2476 1425 5 %
Rwork0.2124 --
obs0.2141 28423 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 63 114 3649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043697
X-RAY DIFFRACTIONf_angle_d0.675050
X-RAY DIFFRACTIONf_dihedral_angle_d11.171387
X-RAY DIFFRACTIONf_chiral_restr0.027550
X-RAY DIFFRACTIONf_plane_restr0.004647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48580.35631220.33732666X-RAY DIFFRACTION100
2.4858-2.58530.38111430.32212645X-RAY DIFFRACTION100
2.5853-2.7030.36371480.28852634X-RAY DIFFRACTION100
2.703-2.84550.32421360.28112657X-RAY DIFFRACTION100
2.8455-3.02370.34491570.28952662X-RAY DIFFRACTION100
3.0237-3.25710.30721430.28012664X-RAY DIFFRACTION100
3.2571-3.58480.2541510.24432690X-RAY DIFFRACTION100
3.5848-4.10330.23151370.18582718X-RAY DIFFRACTION100
4.1033-5.16870.2061590.15922744X-RAY DIFFRACTION100
5.1687-46.82540.2041290.18762918X-RAY DIFFRACTION100
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)
17.75310.03242.18740.99490.14841.4390.101-0.2439-0.41050.01260.00820.08850.164-0.1385-0.10490.33920.0133-0.01950.23920.01680.34677.577769.208718.8766
22.13711.8665-0.03758.5584-1.98041.81340.01370.1701-0.21320.15660.198-0.26210.27710.1391-0.2010.47090.1070.05620.583-0.07750.416436.769556.16952.2381
32.82791.89830.42655.2406-0.87824.4242-0.02650.40220.0177-0.19730.0425-0.18070.03820.3207-0.01930.23410.0220.05080.32820.01750.336532.705481.644212.4583
46.4779-0.7742.52484.25092.04172.6039-0.1721.02010.2161-0.88040.18710.1466-0.32940.44590.00980.6711-0.06580.04190.7350.13860.393129.020577.8365-14.0379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 104 THROUGH 255)
2X-RAY DIFFRACTION2CHAIN B AND (RESID 105 THROUGH 257 )
3X-RAY DIFFRACTION3CHAIN X AND (RESID 19 THROUGH 83 )
4X-RAY DIFFRACTION4CHAIN Y AND (RESID 19 THROUGH 83 )

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