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(-) Description

Title :  CRYSTAL STRUCTURE OF FANCL
 
Authors :  A. R. Cole, H. Walden
Date :  28 Sep 09  (Deposition) - 16 Feb 10  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  A,B  (3x)
Biol. Unit 4:  A,B  (1x)
Keywords :  Ubc, Ring, Rwd, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Cole, L. P. C. Lewis, H. Walden
The Structure Of The Catalytic Subunit Fancl Of The Fanconi Anemia Core Complex
Nat. Struct. Mol. Biol. V. 17 294 2010
PubMed-ID: 20154706  |  Reference-DOI: 10.1038/NSMB.1759

(-) Compounds

Molecule 1 - FANCL
    Chains: B, A
    EC Number: 6.3.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET 28A(+)
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CG12812
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: AT07283P, E3 LIGASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x):  B
Biological Unit 2 (1x): A 
Biological Unit 3 (3x): AB
Biological Unit 4 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric Unit (4, 22)
No.NameCountTypeFull Name
1AU13Ligand/IonGOLD ION
2CIT3Ligand/IonCITRIC ACID
3MAL2Ligand/IonMALTOSE
4ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1AU-1Ligand/IonGOLD ION
2CIT1Ligand/IonCITRIC ACID
3MAL1Ligand/IonMALTOSE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1AU-1Ligand/IonGOLD ION
2CIT2Ligand/IonCITRIC ACID
3MAL1Ligand/IonMALTOSE
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 15)
No.NameCountTypeFull Name
1AU-1Ligand/IonGOLD ION
2CIT9Ligand/IonCITRIC ACID
3MAL6Ligand/IonMALTOSE
4ZN-1Ligand/IonZINC ION
Biological Unit 4 (2, 5)
No.NameCountTypeFull Name
1AU-1Ligand/IonGOLD ION
2CIT3Ligand/IonCITRIC ACID
3MAL2Ligand/IonMALTOSE
4ZN-1Ligand/IonZINC ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS B:329 , CYS B:334 , CYS B:364 , CYS B:367BINDING SITE FOR RESIDUE ZN B 382
02AC2SOFTWARECYS B:311 , CYS B:314 , HIS B:339 , CYS B:342BINDING SITE FOR RESIDUE ZN B 383
03AC3SOFTWARETYR B:289 , PHE B:290 , MET B:292 , ASP B:294 , SER B:296BINDING SITE FOR RESIDUE MAL B 5044
04AC4SOFTWAREGLY B:55 , CYS B:165 , AU B:385BINDING SITE FOR RESIDUE CIT B 2502
05AC5SOFTWARECYS B:125 , GLN B:127BINDING SITE FOR RESIDUE AU B 384
06AC6SOFTWARECYS B:165 , VAL B:166 , CIT B:2502BINDING SITE FOR RESIDUE AU B 385
07AC7SOFTWARECYS B:288BINDING SITE FOR RESIDUE AU B 386
08AC8SOFTWARECYS B:12BINDING SITE FOR RESIDUE AU B 387
09AC9SOFTWARELEU B:22 , CYS B:28BINDING SITE FOR RESIDUE AU B 388
10BC1SOFTWARETYR A:119 , TYR B:119BINDING SITE FOR RESIDUE AU B 389
11BC2SOFTWAREASN B:199 , CYS B:242 , ILE B:243 , ILE B:277BINDING SITE FOR RESIDUE AU B 390
12BC3SOFTWAREGLU A:8 , LEU A:11 , CYS A:12 , THR B:349BINDING SITE FOR RESIDUE AU B 391
13BC4SOFTWARECYS A:329 , CYS A:334 , CYS A:364 , CYS A:367BINDING SITE FOR RESIDUE ZN A 382
14BC5SOFTWARECYS A:311 , CYS A:314 , HIS A:339 , CYS A:342BINDING SITE FOR RESIDUE ZN A 383
15BC6SOFTWARETYR A:289 , MET A:292 , ASP A:294 , SER A:296 , ASP A:297BINDING SITE FOR RESIDUE MAL A 5045
16BC7SOFTWAREILE A:29 , LYS A:44 , TYR A:46 , GLN A:57BINDING SITE FOR RESIDUE CIT A 2503
17BC8SOFTWAREGLU A:65 , LYS A:75 , CYS A:165 , ALA A:237 , AU A:385BINDING SITE FOR RESIDUE CIT A 2504
18BC9SOFTWARECYS A:125 , GLN A:127BINDING SITE FOR RESIDUE AU A 384
19CC1SOFTWARECYS A:165 , VAL A:166 , PRO A:239 , CIT A:2504BINDING SITE FOR RESIDUE AU A 385
20CC2SOFTWARECYS A:288BINDING SITE FOR RESIDUE AU A 386
21CC3SOFTWARECYS A:12BINDING SITE FOR RESIDUE AU A 387
22CC4SOFTWAREVAL A:7 , ALA A:20 , LEU A:22 , CYS A:28BINDING SITE FOR RESIDUE AU A 388

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:311 -A:314
2A:311 -A:342
3A:314 -A:342
4A:329 -A:334
5A:329 -A:364
6B:311 -B:314
7B:314 -B:342
8B:329 -B:364

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1His B:50 -Pro B:51
2Ile B:152 -Pro B:153
3Gln B:211 -Pro B:212
4His A:50 -Pro A:51
5Ile A:152 -Pro A:153
6Gln A:211 -Pro A:212

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K1L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K1L)

(-) Exons   (0, 0)

(no "Exon" information available for 3K1L)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:376
 aligned with Q8T913_DROME | Q8T913 from UniProtKB/TrEMBL  Length:381

    Alignment length:377
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       
         Q8T913_DROME     5 EDVERLLCQKYPGLAAELQPSGACIIRGVLGSEDTWRRLKLYLPHHPALHGFQLYVQESLEYKLYTSANLKLQDDWLLEDFLDHLPKILPAQKAPTVPKELCREGNIYYDILALYKSNEYCLQVDEACSMIRFSEFTDFEQHYLELKIPSLLLLDHSLPDCVSLGEMLTKSAGNLEEALNLFRKLLEDLRPFYDNFMDIDELCHVLQPSPISSKHKTRLFPLKDRVYLKLTIADPFACIASMSLKIIGPTEEVARLRHVLSDGLSNWDSEMNIHKNLLRMFDLCYFPMPDWSDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTSFAALLND 381
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..eeeee.....eeeeeeeee..eeeeeeeee.........eeeeee..eeeee...........hhhhhhhhhhhhh.........-.hhhhhhhhhhhhhhhh....eeee.hhh.eeeeeee..eeeeeeeee.....eeee......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeee..eeeeeee.........eeeeee.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.......hhhhh.........................................hhhhhhhhhhhhh........eee......eee.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k1l A   5 EDVERLLCQKYPGLAAELQPSGACIIRGVLGSEDTWRRLKLYLPHHPALHGFQLYVQESLEYKLYTSANLKLQDDWLLEDFLDHLPKILPAQKAPTVP-ELCREGNIYYDILALYKSNEYCLQVDEACSMIRFSEFTDFEQHYLELKIPSLLLLDHSLPDCVSLGEMLTKSAGNLEEALNLFRKLLEDLRPFYDNFMDIDELCHVLQPSPISSKHKTRLFPLKDRVYLKLTIADPFACIASMSLKIIGPTEEVARLRHVLSDGLSNWDSEMNIHKNLLRMFDLCYFPMPDWSDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTSFAALLND 381
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       
                                                                                                                           102 |                                                                                                                                                                                                                                                                                     
                                                                                                                             104                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:364
 aligned with Q8T913_DROME | Q8T913 from UniProtKB/TrEMBL  Length:381

    Alignment length:376
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375      
         Q8T913_DROME     6 DVERLLCQKYPGLAAELQPSGACIIRGVLGSEDTWRRLKLYLPHHPALHGFQLYVQESLEYKLYTSANLKLQDDWLLEDFLDHLPKILPAQKAPTVPKELCREGNIYYDILALYKSNEYCLQVDEACSMIRFSEFTDFEQHYLELKIPSLLLLDHSLPDCVSLGEMLTKSAGNLEEALNLFRKLLEDLRPFYDNFMDIDELCHVLQPSPISSKHKTRLFPLKDRVYLKLTIADPFACIASMSLKIIGPTEEVARLRHVLSDGLSNWDSEMNIHKNLLRMFDLCYFPMPDWSDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTSFAALLND 381
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----WD-3-3k1lB03 B:11-293                                                                                                                                                                                                                                                                      -------------FANCL_C-3k1lB01 B:307-376                                             ----- Pfam domains (1)
           Pfam domains (2) -----WD-3-3k1lB04 B:11-293                                                                                                                                                                                                                                                                      -------------FANCL_C-3k1lB02 B:307-376                                             ----- Pfam domains (2)
         Sec.struct. author hhhhhhhhhh..eeeee.....eeeeeeeee..eeeeeeeee.........eeeee....eeee...........hhhhhhhhhhhhh.------------...hhhhhhhhhhh....eeee.hhh.eeeeeee..eeeeeeeee.....eeee......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeee..eeeeeee.........eeeeee.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhh........hhhhh.........................................hhhhhhhhhhhhh........eee......eee.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k1l B   6 DVERLLCQKYPGLAAELQPSGACIIRGVLGSEDTWRRLKLYLPHHPALHGFQLYVQESLEYKLYTSANLKLQDDWLLEDFLDHLPKILP------------REGNIYYDILALYKSNEYCLQVDEACSMIRFSEFTDFEQHYLELKIPSLLLLDHSLPDCVSLGEMLTKSAGNLEEALNLFRKLLEDLRPFYDNFMDIDELCHVLQPSPISSKHKTRLFPLKDRVYLKLTIADPFACIASMSLKIIGPTEEVARLRHVLSDGLSNWDSEMNIHKNLLRMFDLCYFPMPDWSDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTSFAALLND 381
                                    15        25        35        45        55        65        75        85        |-         - |     115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375      
                                                                                                                   94          107
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3K1L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K1L)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: RING (39)
(-)
Clan: no clan defined [family: WD-3] (1)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8T913_DROME | Q8T913)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006513    protein monoubiquitination    Addition of a single ubiquitin group to a protein.
cellular component
    GO:0043240    Fanconi anaemia nuclear complex    A protein complex composed of the Fanconi anaemia (FA) proteins including A, C, E, G and F (FANCA-F). Functions in the activation of the downstream protein FANCD2 by monoubiquitylation, and is essential for protection against chromosome breakage.
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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