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(-) Description

Title :  RAN Y39A IN COMPLEX WITH GPPNHP AND RANBD1
 
Authors :  I. R. Vetter, S. Brucker
Date :  16 Jul 15  (Deposition) - 09 Sep 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Gtpase, Nuclear Transport, Hydrolase, Ran Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Rudack, S. Jenrich, S. Brucker, I. R. Vetter, K. Gerwert, C. Kotting
Catalysis Of Gtp Hydrolysis By Small Gtpases At Atomic Detail By Integration Of X-Ray Crystallography, Experimental, And Theoretical Ir Spectroscopy.
J. Biol. Chem. V. 290 24079 2015
PubMed-ID: 26272610  |  Reference-DOI: 10.1074/JBC.M115.648071

(-) Compounds

Molecule 1 - GTP-BINDING NUCLEAR PROTEIN RAN
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET3D
    Expression System Taxid469008
    GeneRAN, ARA24, OK/SW-CL.81
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymANDROGEN RECEPTOR-ASSOCIATED PROTEIN 24,GTPASE RAN,RAS-LIKE PROTEIN TC4,RAS-RELATED NUCLEAR PROTEIN
 
Molecule 2 - E3 SUMO-PROTEIN LIGASE RANBP2
    ChainsB, D
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX4T1
    Expression System Taxid469008
    FragmentRAN BINDING DOMAIN 1, UNP RESIDUES 1155-1321
    GeneRANBP2, NUP358
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym358 KDA NUCLEOPORIN,NUCLEAR PORE COMPLEX PROTEIN NUP358, NUCLEOPORIN NUP358,RAN-BINDING PROTEIN 2,RANBP2,P270

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
3SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO43Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:18 , GLY A:19 , GLY A:20 , THR A:21 , GLY A:22 , LYS A:23 , THR A:24 , THR A:25 , GLU A:36 , LYS A:37 , LYS A:38 , ALA A:39 , ALA A:41 , THR A:42 , ALA A:67 , 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:401binding site for residue GNP A 301
02AC2SOFTWARETHR A:24 , THR A:42 , GNP A:301 , HOH A:401binding site for residue MG A 302
03AC3SOFTWAREPRO A:102 , PHE A:138 , ARG A:140binding site for residue SO4 A 303
04AC4SOFTWAREGLU C:70binding site for residue SO4 A 304
05AC5SOFTWAREARG B:49 , ASP B:119binding site for residue SO4 B 201
06AC6SOFTWARETYR A:147 , ARG A:166 , LYS C:37binding site for residue SO4 C 301
07AC7SOFTWAREGLY C:19 , GLY C:20 , THR C:21 , GLY C:22 , LYS C:23 , THR C:24 , THR C:25 , GLU C:36 , LYS C:37 , LYS C:38 , ALA C:39 , ALA C:41 , THR C:42 , GLY C:68 , ASN C:122 , LYS C:123 , ASP C:125 , ILE C:126 , ALA C:151 , LYS C:152 , MG C:303 , HOH C:401 , HOH C:402 , HOH C:404binding site for residue GNP C 302
08AC8SOFTWARETHR C:24 , THR C:42 , GNP C:302 , HOH C:402 , HOH C:404binding site for residue MG C 303
09AC9SOFTWAREGLY D:105 , SER D:106 , ASP D:107 , ARG D:108binding site for residue SO4 D 201
10AD1SOFTWAREASN D:64 , LYS D:66 , ARG D:81binding site for residue SO4 D 202

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1B:142 -B:142
2D:142 -D:142

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val D:22 -Pro D:23
2Leu D:151 -Lys D:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CLQ)

(-) 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:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee........hhhhhh....eeeeeee..hhhhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhh..eeeee.........hhhhhhhhhhhhh......................hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5clq A   5 GEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKAVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPD 211
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       

Chain B from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeeeeeeeeeeee....eeeeeeeeeeeeeee.....eeeeeee.....eeeeee.......ee......eeeeeeee......eeeeeeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5clq B  19 EPVVPLPDKIEVKTGEEDEEEFFCNRAKLFRFDVESKEWKERGIGNVKILRHKTSGKIRLLMRREQVLKICANHYISPDMKLTPNAGSDRSFVWHALDYADELPKPEQLAIRFKTPEEAALFKCKFEEAQSILK 152
                                    28        38        48        58        68        78        88        98       108       118       128       138       148    

Chain C from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..................eeeeeee..hhhhhhhhhhhhhhhhh......eeeeee.........hhhhh....eeee.........hhhhhhhhhhhhh......................hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5clq C   8 QVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKAVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPD 211
                                    17        27        37        47        57        67        77        87        97       107       117       127       137 ||    151       161       171       181       191       201       211
                                                                                                                                                             139|                                                                   
                                                                                                                                                              144                                                                   

Chain D from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeeeeeeeee....eeeeeeeeeeeeee......eeeeee......eeeeee.......ee......eeeeeeee......eeeeeeee..hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5clq D  22 VPLPDKIEVKTGEEDEEEFFCNRAKLFRFDVESKEWKERGIGNVKILRHKTSGKIRLLMRREQVLKICANHYISPDMKLTPNAGSDRSFVWHALDYADELPKPEQLAIRFKTPEEAALFKCKFEEAQSILK 152
                                    31        41        51        61        71        81        91       101       111       121       131       141       151 

   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 5CLQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (93, 105)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAN_HUMAN | P628261i2m 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 5dh9 5dha 5dhf 5di9 5dif 5dis 5dlq 5fyq 5jlj 5uwh 5uwi 5uwj 5uwo 5uwp 5uwq 5uwr 5uws 5uwt 5uwu 5uww
        RBP2_HUMAN | P497921rrp 1xke 1z5s 2las 3uin 3uio 3uip 4ga0 4i9y 4l6e 4lqw 5cll

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5CLQ)