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(-) Description

Title :  HUMAN ATLASTIN-1 1-446, N440T, GPPNHP
 
Authors :  L. J. Byrnes, A. Singh, K. Szeto, N. M. Benvin, J. P. O'Donnell, W. R. Zipf H. Sondermann
Date :  12 Dec 12  (Deposition) - 09 Jan 13  (Release) - 20 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Gtpase, Gtp/Gdp Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Byrnes, A. Singh, K. Szeto, N. M. Benvin, J. P. O'Donnell, W. R. Zipfel, H. Sondermann
Structural Basis For Conformational Switching And Gtp Loading Of The Large G Protein Atlastin.
Embo J. V. 32 369 2013
PubMed-ID: 23334294  |  Reference-DOI: 10.1038/EMBOJ.2012.353

(-) Compounds

Molecule 1 - ATLASTIN-1
    Chains: A, B, C, D
    EC Number: 3.6.5.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: CYTOPLASMIC DOMAIN (UNP RESIDUES 1-446)
    Gene: ATL1, GBP3, SPG3A
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BRAIN-SPECIFIC GTP-BINDING PROTEIN, GTP-BINDING PROTEIN 3, GBP-3, HGBP3, GUANINE NUCLEOTIDE-BINDING PROTEIN 3, SPASTIC PARAPLEGIA 3 PROTEIN A

 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, 44)

Asymmetric Unit (3, 44)
No.NameCountTypeFull Name
1GNP4Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG4Ligand/IonMAGNESIUM ION
3MSE36Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 20)
No.NameCountTypeFull Name
1GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3MSE18Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 20)
No.NameCountTypeFull Name
1GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:76 , ARG A:77 , LYS A:78 , GLY A:79 , LYS A:80 , SER A:81 , PHE A:82 , TRP A:112 , ARG A:113 , GLY A:114 , ARG A:118 , GLU A:119 , THR A:120 , GLY A:149 , ARG A:217 , ASP A:218 , PRO A:272 , VAL A:276 , PHE A:282 , MG A:502 , HOH A:601 , HOH A:602 , HOH A:611 , HOH A:616 , HOH A:708BINDING SITE FOR RESIDUE GNP A 501
2AC2SOFTWARESER A:81 , THR A:120 , GNP A:501 , HOH A:601 , HOH A:708BINDING SITE FOR RESIDUE MG A 502
3AC3SOFTWAREPHE B:76 , ARG B:77 , LYS B:78 , GLY B:79 , LYS B:80 , SER B:81 , PHE B:82 , TRP B:112 , ARG B:113 , GLY B:114 , ARG B:118 , GLU B:119 , THR B:120 , GLY B:149 , ARG B:217 , ASP B:218 , HIS B:271 , PRO B:272 , VAL B:276 , PHE B:282 , PHE B:293 , MG B:502 , HOH B:601 , HOH B:602 , HOH B:611 , HOH B:676 , HOH B:689BINDING SITE FOR RESIDUE GNP B 501
4AC4SOFTWARESER B:81 , THR B:120 , GNP B:501 , HOH B:601 , HOH B:689BINDING SITE FOR RESIDUE MG B 502
5AC5SOFTWAREPHE C:76 , ARG C:77 , LYS C:78 , GLY C:79 , LYS C:80 , SER C:81 , PHE C:82 , TRP C:112 , ARG C:113 , GLY C:114 , ARG C:118 , GLU C:119 , THR C:120 , GLY C:149 , ARG C:217 , ASP C:218 , HIS C:271 , PRO C:272 , VAL C:276 , PHE C:282 , MG C:502 , HOH C:601 , HOH C:602BINDING SITE FOR RESIDUE GNP C 501
6AC6SOFTWARESER C:81 , THR C:120 , GNP C:501 , HOH C:601 , HOH C:692BINDING SITE FOR RESIDUE MG C 502
7AC7SOFTWAREPHE D:76 , ARG D:77 , LYS D:78 , GLY D:79 , LYS D:80 , SER D:81 , PHE D:82 , TRP D:112 , ARG D:113 , GLY D:114 , ARG D:118 , GLU D:119 , THR D:120 , GLY D:149 , ARG D:217 , ASP D:218 , HIS D:271 , PRO D:272 , VAL D:276 , PHE D:282 , MG D:502 , HOH D:601 , HOH D:608 , HOH D:609 , HOH D:641 , HOH D:695BINDING SITE FOR RESIDUE GNP D 501
8AC8SOFTWARESER D:81 , THR D:120 , ASP D:146 , GNP D:501 , HOH D:601 , HOH D:695BINDING SITE FOR RESIDUE MG D 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IDP)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Mse B:408 -Gly B:409
2Mse C:408 -Gly C:409

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IDP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IDP)

(-) Exons   (0, 0)

(no "Exon" information available for 4IDP)

(-) 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:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....eeehhhhhhhhhh........eeeeeeee....hhhhhhhhhhhhhhhh............................eeee...eeee.....eeeeeeeee........hhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhh........eeeeeeeee..........hhhhhhhhhhhhh......hhhhhhhhhhhhhheeeeeeee....hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4idp A  31 KAGPVQVLIVKDDHSFELDETALNRILLSEAVRDKEVVAVSVAGAFRKGKSFLmDFmLRYmYNQESVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEIFLINKPDGKKVAVLLmDTQGTFDSQSTLRDSATVFALSTmISSIQVYNLSQNVQEDDLQHLQLFTEYGRLAmEETFLKPFQSLIFLVRDWSFPYEFSYGADGGAKFLEKRLKVSGNQHEELQNVRKHIHSCFTNISCFLLPHPGLKVATNPNFDGKLKEIDDEFIKNLKILIPWLLSPESLDIKEINGNKITCRGLVEYFKAYIKIYQGEELPHPKSmLQATAEANNLAAVATAKDTYNKKmEEICGGDKPFLAPNDLQTKHLQLKEESVKLFRGVKKmGGEEFSRRYLQQLESEIDELYIQYIKHNDSKTIFHAAR 446
                                    40        50        60        70        80   |  | 90|      100       110       120       130       140    |  150       160       170       180       190       200|      210       220       230       240       250       260       270       280       290       300       310       320       330       340      |350       360       370|      380       390       400       410       420       430       440      
                                                                                84-MSE  |                                                   145-MSE                 169-MSE                         201-MSE                                                                                                                                           347-MSE                 371-MSE                              408-MSE                                  
                                                                                   87-MSE                                                                                                                                                                                                                                                                                                                                                                   
                                                                                       91-MSE                                                                                                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....eeehhhhhhhhhh.......eeeeeeeee....hhhhhhhhhhhhhhhh............................eeee...eeee.....eeeeeeeee........hhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhh.........eeeeeeeee..........hhhhhhhhhhhhh......hhhhhhhhhhhhhheeeeeeee....hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4idp B  31 KAGPVQVLIVKDDHSFELDETALNRILLSEAVRDKEVVAVSVAGAFRKGKSFLmDFmLRYmYNQESVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEIFLINKPDGKKVAVLLmDTQGTFDSQSTLRDSATVFALSTmISSIQVYNLSQNVQEDDLQHLQLFTEYGRLAmEETFLKPFQSLIFLVRDWSFPYEFSYGADGGAKFLEKRLKVSGNQHEELQNVRKHIHSCFTNISCFLLPHPGLKVATNPNFDGKLKEIDDEFIKNLKILIPWLLSPESLDIKEINGNKITCRGLVEYFKAYIKIYQGEELPHPKSmLQATAEANNLAAVATAKDTYNKKmEEICGGDKPFLAPNDLQTKHLQLKEESVKLFRGVKKmGGEEFSRRYLQQLESEIDELYIQYIKHNDSKTIFHAAR 446
                                    40        50        60        70        80   |  | 90|      100       110       120       130       140    |  150       160       170       180       190       200|      210       220       230       240       250       260       270       280       290       300       310       320       330       340      |350       360       370|      380       390       400       410       420       430       440      
                                                                                84-MSE  |                                                   145-MSE                 169-MSE                         201-MSE                                                                                                                                           347-MSE                 371-MSE                              408-MSE                                  
                                                                                   87-MSE                                                                                                                                                                                                                                                                                                                                                                   
                                                                                       91-MSE                                                                                                                                                                                                                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....eeehhhhhhhhhh........eeeeeeee....hhhhhhhhhhhhhhhh............................eeee...eeee.....eeeeeeeee........hhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhh........eeeeeeeee..........hhhhhhhhhhhhh......hhhhhhhhhhhhhheeeeeeee....hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4idp C  31 KAGPVQVLIVKDDHSFELDETALNRILLSEAVRDKEVVAVSVAGAFRKGKSFLmDFmLRYmYNQESVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEIFLINKPDGKKVAVLLmDTQGTFDSQSTLRDSATVFALSTmISSIQVYNLSQNVQEDDLQHLQLFTEYGRLAmEETFLKPFQSLIFLVRDWSFPYEFSYGADGGAKFLEKRLKVSGNQHEELQNVRKHIHSCFTNISCFLLPHPGLKVATNPNFDGKLKEIDDEFIKNLKILIPWLLSPESLDIKEINGNKITCRGLVEYFKAYIKIYQGEELPHPKSmLQATAEANNLAAVATAKDTYNKKmEEICGGDKPFLAPNDLQTKHLQLKEESVKLFRGVKKmGGEEFSRRYLQQLESEIDELYIQYIKHNDSKTIFHAAR 446
                                    40        50        60        70        80   |  | 90|      100       110       120       130       140    |  150       160       170       180       190       200|      210       220       230       240       250       260       270       280       290       300       310       320       330       340      |350       360       370|      380       390       400       410       420       430       440      
                                                                                84-MSE  |                                                   145-MSE                 169-MSE                         201-MSE                                                                                                                                           347-MSE                 371-MSE                              408-MSE                                  
                                                                                   87-MSE                                                                                                                                                                                                                                                                                                                                                                   
                                                                                       91-MSE                                                                                                                                                                                                                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....eeehhhhhhhhhh........eeeeeeee....hhhhhhhhhhhhhhhh............................eeee...eeee.....eeeeeeeee........hhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhh........eeeeeeeee..........hhhhhhhhhhhhh......hhhhhhhhhhhhhheeeeeeee....hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4idp D  30 KKAGPVQVLIVKDDHSFELDETALNRILLSEAVRDKEVVAVSVAGAFRKGKSFLmDFmLRYmYNQESVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEIFLINKPDGKKVAVLLmDTQGTFDSQSTLRDSATVFALSTmISSIQVYNLSQNVQEDDLQHLQLFTEYGRLAmEETFLKPFQSLIFLVRDWSFPYEFSYGADGGAKFLEKRLKVSGNQHEELQNVRKHIHSCFTNISCFLLPHPGLKVATNPNFDGKLKEIDDEFIKNLKILIPWLLSPESLDIKEINGNKITCRGLVEYFKAYIKIYQGEELPHPKSmLQATAEANNLAAVATAKDTYNKKmEEICGGDKPFLAPNDLQTKHLQLKEESVKLFRGVKKmGGEEFSRRYLQQLESEIDELYIQYIKHNDSKTIFHAAR 446
                                    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 |     379       389       399       409       419       429       439       
                                                                                 84-MSE  |                                                   145-MSE                 169-MSE                         201-MSE                                                                                                                                           347-MSE                 371-MSE                              408-MSE                                  
                                                                                    87-MSE                                                                                                                                                                                                                                                                                                                                                                   
                                                                                        91-MSE
   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 4IDP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IDP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IDP)

(-) Gene Ontology  (19, 19)

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 Related Entries

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        ATLA1_HUMAN | Q8WXF7: 3q5d 3q5e 3qnu 3qof 4idn 4ido 4idq

(-) Related Entries Specified in the PDB File

3q5d 3q5e 4idn 4ido 4idq