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(-) Description

Title :  CRYSTAL STRUCTURE OF CDC7 NES PEPTIDE (EXTENDED) IN COMPLEX WITH CRM1-RAN-RANBP1
 
Authors :  H. Y. J. Fung, Y. M. Chook
Date :  21 Feb 17  (Deposition) - 22 Mar 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Heat Repeat, Nes, Nuclear Export, Karyopherin, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Y. Fung, S. C. Fu, Y. M. Chook
Nuclear Export Receptor Crm1 Recognizes Diverse Conformations In Nuclear Export Signals.
Elife V. 6 2017
PubMed-ID: 28282025  |  Reference-DOI: 10.7554/ELIFE.23961

(-) Compounds

Molecule 1 - GTP-BINDING NUCLEAR PROTEIN RAN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RAN, ARA24, OK/SW-CL.81
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ANDROGEN RECEPTOR-ASSOCIATED PROTEIN 24, GTPASE RAN, RAS- LIKE PROTEIN TC4, RAS-RELATED NUCLEAR PROTEIN
 
Molecule 2 - RAN-SPECIFIC GTPASE-ACTIVATING PROTEIN 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-4T3-TEV
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: CHROMOSOME STABILITY PROTEIN 20, PERINUCLEAR ARRAY-LOCALIZED PROTEIN, RAN-BINDING PROTEIN 1, RANBP1
 
Molecule 3 - EXPORTIN-1
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-4T3-TEV
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CRM1, KAP124, XPO1, YGR218W, G8514
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: CHROMOSOME REGION MAINTENANCE PROTEIN 1, KARYOPHERIN-124
 
Molecule 4 - CELL DIVISION CYCLE 7-RELATED PROTEIN KINASE
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMAL-TEV
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CDC7, CDC7L1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HUCDC7

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3GOL3Ligand/IonGLYCEROL
4MG1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:19 , GLY A:20 , THR A:21 , GLY A:22 , LYS A:23 , THR A:24 , THR A:25 , PHE A:35 , GLU A:36 , LYS A:37 , LYS A:38 , TYR A:39 , ALA A:41 , THR A:42 , GLY A:68 , ASN A:122 , LYS A:123 , ASP A:125 , ILE A:126 , SER A:150 , ALA A:151 , LYS A:152 , MG A:302 , HOH A:416 , HOH A:428 , HOH A:432 , HOH A:435 , HOH A:463binding site for residue GNP A 301
2AC2SOFTWARETHR A:24 , THR A:42 , GNP A:301 , HOH A:416 , HOH A:428binding site for residue MG A 302
3AC3SOFTWAREASN A:103 , TRP A:104 , ASP A:107 , HOH A:403binding site for residue GOL A 303
4AC4SOFTWAREASN C:846 , ASP C:887binding site for residue GOL C 1101
5AC5SOFTWAREGLY C:204 , SER C:207 , SER C:245 , THR C:248binding site for residue GOL C 1102
6AC6SOFTWAREGLU C:355 , ARG C:356 , ASN C:434binding site for residue CL C 1103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5UWR)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp C:130 -Pro C:131

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5UWR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UWR)

(-) Exons   (0, 0)

(no "Exon" information available for 5UWR)

(-) Sequences/Alignments

Asymmetric/Biological 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:204
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhh.hhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeee.........hhhhh.hhhhhh.eeee.........hhhhhhhhhhhhh..................hhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5uwr A    9 VQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVALAAQYEHDLEVAQTTALPDEDDDL  216
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       192       202       212    
                                                                                                                                                                                                            187|                        
                                                                                                                                                                                                             192                        


Chain B from PDB  Type:PROTEIN  Length:127
                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeeeeeee....eeeeeeeeeeeeeee.....eeeeee......eeeeee.......eee..eeeeeeeee...........eeeeee..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                5uwr B   64 HFEPVMEEDEEVLYKVRAKLFRFDADAKEWKERGTGDCKFLKNKKTNKVRILMRRDKTLKICANHIIAPEYTLKPNVGSDRSWVYACTADIAEGEAEAFTFAIRFGSKENADKFKEEFEKAQEINKK  200
                                ||  83        93       103       113       123       133       143       153       163       173       183       193       
                               68|                                                                                                                         
                                79                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:1000
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5uwr C    0 SMEGILDFSNDLDIALLDQVVSTFYQGSGVQQKQAQEILTKFQDNPDAWQKADQILQFSTNPQSKFIALSILDKLITRKWKLLPNDHRIGIRNFVVGMIISMCQDDEVFKTQKNLINKSDLTLVQILKQEWPQNWPEFIPELIGSSSSSVNVCENNMIVLKLLSEEVFDFSAEQMTQAKALHLKNSMSKEFEQIFKLCFQVLEQGSSSSLIVATLESLLRYLHWIPYRYIYETNILELLSTKFMTSPDTRAITLKCLTEVSNLKIPQDNDLIKRQTVLFFQNTLQQIATSVMPVTADLKATYANANGNDQSFLQDLAMFLTTYLARNRALLESDESLRELLLNAHQYLIQLSKIEERELFKTTLDYWHNLVADLFYEPLKKHIYEEICSQLRLVIIENMVRPEEKESDTIQLYKSEREVLVYLTHLNVIDTEEIMISKLARQIDGSEWSWHNINTLSWAIGSISGTMSEDTEKRFVVTVIKDLLGLCEQKRGKDNKAVVASDIMYVVGQYPRFLKAHWNFLRTVILKLFEFMHETHEGVQDMACDTFIKIVQKCKYHFVIQQPRESEPFIQTIIRDIQKTTADLQPQQVHTFYKACGIIISEERSVAERNRLLSDLMQLPNMAWDTIVEQSTANPTLLLDSETVKIIANIIKTNVAVCTSMGADFYPQLGHIYYNMLQLYRAVSSMISAQVAAEGLIATKTPKVRGLRTIKKEILKLVETYISKARNLDDVVKVLVEPLLNAVLEDYMNNVPDARDAEVLNCMTTVVEKVGHMIPQGVILILQSVFECTLDMINKDFTEYPEHRVEFYKLLKVINEKSFAAFLELPPAAFKLFVDAICWAFKHNNRDVEVNGLQIALDLVKNIERMGNVPFANEFHKNYFFIFVSETFFVLTDSDHKSGFSKQALLLMKLISLVYDNKISVPLYQEAEVPQGTSNQVYLSQYLANMLSNAFPHLTSEQIASFLSALTKQCKDLVVFKGTLRDFLVQIKEVGGDPTDYLFA 1052
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369      |416       426       436   ||  462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052
                                                                                                                                                                                                                                                                                                                                                                                                                  376|                       440|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                                                                                                                   414                        457                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:12
                                             
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                5uwr D  457 DLRKLCERLRGM  468
                                   466
   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 5UWR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UWR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UWR)

(-) Gene Ontology  (102, 124)

Asymmetric/Biological Unit(hide GO term definitions)

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  5uwr
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  CDC7_HUMAN | O00311
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  RAN_HUMAN | P62826
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  XPO1_YEAST | P30822
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  YRB1_YEAST | P41920
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CDC7_HUMAN | O00311: 4f99 4f9a 4f9b 4f9c 5uwq
        RAN_HUMAN | P62826: 1i2m 1ibr 1k5d 1k5g 1qbk 1rrp 2mmc 2mmg 2n1b 3ch5 3ea5 3gj0 3gj3 3gj4 3gj5 3gj6 3gj7 3gj8 3gjx 3nby 3nbz 3nc0 3nc1 3zjy 4c0q 4gmx 4gpt 4hat 4hau 4hav 4haw 4hax 4hay 4haz 4hb0 4hb2 4hb3 4hb4 4ol0 4wvf 5ciq 5cit 5ciw 5cj2 5cll 5clq 5dh9 5dha 5dhf 5di9 5dif 5dis 5dlq 5fyq 5jlj 5uwh 5uwi 5uwj 5uwo 5uwp 5uwq 5uws 5uwt 5uwu 5uww
        XPO1_YEAST | P30822: 3m1i 3vyc 3wyf 3wyg 4gmx 4gpt 4hat 4hau 4hav 4haw 4hax 4hay 4haz 4hb0 4hb2 4hb3 4hb4 5dh9 5dha 5dhf 5di9 5dif 5jlj 5uwh 5uwi 5uwj 5uwo 5uwp 5uwq 5uws 5uwt 5uwu 5uww
        YRB1_YEAST | P41920: 3m1i 4gmx 4gpt 4hat 4hau 4hav 4haw 4hax 4hay 4haz 4hb0 4hb2 4hb3 4hb4 4wvf 5dh9 5dha 5dhf 5di9 5dif 5jlj 5uwh 5uwi 5uwj 5uwo 5uwp 5uwq 5uws 5uwt 5uwu 5uww

(-) Related Entries Specified in the PDB File

5uwh 5uwi 5uwj 5uwo 5uwp 5uwq 5uws 5uwt 5uwu 5uww