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(-) Description

Title :  AMINO TERMINAL DOMAIN OF THE N-ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN (NSF)
 
Authors :  A. P. May, K. M. S. Misura, S. W. Whiteheart, W. I. Weis
Date :  21 May 99  (Deposition) - 21 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (2x)
Keywords :  Double-Psi Beta Barrel Alpha/Beta Barrel, Vesicular-Fusion Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. May, K. M. Misura, S. W. Whiteheart, W. I. Weis
Crystal Structure Of The Amino-Terminal Domain Of N-Ethylmaleimide-Sensitive Fusion Protein.
Nat. Cell Biol. V. 1 175 1999
PubMed-ID: 10559905  |  Reference-DOI: 10.1038/11097
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (N-ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN (NSF))
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE9
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: AMINO TERMINAL DOMAIN
    Organ: OVARY
    Organism Common: CHINESE HAMSTER
    Organism Scientific: CRICETULUS GRISEUS
    Organism Taxid: 10029

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1BME6Ligand/IonBETA-MERCAPTOETHANOL
2SO48Ligand/IonSULFATE ION
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1BME6Ligand/IonBETA-MERCAPTOETHANOL
2SO48Ligand/IonSULFATE ION
Biological Unit 2 (2, 28)
No.NameCountTypeFull Name
1BME12Ligand/IonBETA-MERCAPTOETHANOL
2SO416Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:10 , CYS A:11 , PHE A:62 , ARG A:67 , HOH A:534 , HOH A:557BINDING SITE FOR RESIDUE SO4 A 501
02AC2SOFTWARETHR A:13 , HIS A:52 , HOH A:506 , THR B:13 , HIS B:52 , HOH B:513 , HOH B:547 , HIS C:52BINDING SITE FOR RESIDUE SO4 A 502
03AC3SOFTWAREARG B:10 , CYS B:11 , PHE B:62 , ARG B:67 , HOH B:537BINDING SITE FOR RESIDUE SO4 B 503
04AC4SOFTWAREARG C:10 , CYS C:11 , ARG C:67 , HOH C:541BINDING SITE FOR RESIDUE SO4 C 504
05AC5SOFTWARESER A:73 , ILE A:74 , HOH A:583 , HOH A:595 , LYS B:150BINDING SITE FOR RESIDUE SO4 A 505
06AC6SOFTWARELYS A:150 , ARG B:10 , ARG B:67 , HOH B:578BINDING SITE FOR RESIDUE SO4 B 506
07AC7SOFTWAREARG B:38 , PRO B:41BINDING SITE FOR RESIDUE SO4 B 507
08AC8SOFTWARESER C:73 , ILE C:74 , HOH C:560 , HOH C:573BINDING SITE FOR RESIDUE SO4 C 508
09AC9SOFTWARECYS A:11 , PRO A:12 , LEU A:16 , SER A:17 , SER A:19 , CYS A:21 , VAL A:23 , ALA A:61 , PHE A:62 , SER A:63 , GLN A:66BINDING SITE FOR RESIDUE BME A 400
10BC1SOFTWAREPHE A:85 , LYS A:87 , GLN A:90 , CYS A:91 , LEU A:176 , HOH A:517 , HOH A:596 , GLY B:179BINDING SITE FOR RESIDUE BME A 401
11BC2SOFTWARECYS B:11 , PRO B:12 , LEU B:16 , SER B:17 , SER B:19 , CYS B:21 , VAL B:23 , ALA B:61 , PHE B:62 , SER B:63 , GLN B:66BINDING SITE FOR RESIDUE BME B 400
12BC3SOFTWAREGLY A:179 , PHE B:85 , LYS B:87 , GLN B:90 , CYS B:91 , LEU B:176BINDING SITE FOR RESIDUE BME B 401
13BC4SOFTWARECYS C:11 , PRO C:12 , LEU C:16 , SER C:17 , SER C:19 , CYS C:21 , VAL C:23 , ALA C:61 , PHE C:62 , SER C:63 , GLN C:66BINDING SITE FOR RESIDUE BME C 400
14BC5SOFTWAREPHE C:85 , LYS C:87 , GLN C:90 , CYS C:91 , LEU C:176 , GLY C:179 , HOH C:525BINDING SITE FOR RESIDUE BME C 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QDN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QDN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QDN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QDN)

(-) Exons   (0, 0)

(no "Exon" information available for 1QDN)

(-) 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:189
 aligned with NSF_CRIGR | P18708 from UniProtKB/Swiss-Prot  Length:744

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
            NSF_CRIGR     1 MAGRSMQAARCPTDELSLSNCAVVSEKDYQSGQHVIVRTSPNHKYIFTLRTHPSVVPGSVAFSLPQRKWAGLSIGQEIEVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKMAAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMDPSILKGEPASGKRQKIEVGLVVGNSQVAFEKAENSSLNLIGKAKT 201
               SCOP domains d1qdna1 A:1-85 N-terminal domain of NSF-N, NSF-Nn                                    d1qdna2 A:86-201 C-terminal domain of NSF-N, NSF-Nc                                                                  SCOP domains
               CATH domains 1qdnA01 A:1-83  [code=2.40.40.20, no name defined]                                 1qdnA02 A:84-201  [code=3.10.330.10, no name defined]                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhh...eee.........eeeeeee..eeeeeeeee.......eee.hhhhhhhhh.....eeeeeee...hhhh...eeeeeeee.hhhhh...eeehhhhhhhhhhhhh..eee...eeeeee..eeeeeeeeeee....------------....eee.....eeeeee......eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qdn A   1 MAGRSMQAARCPTDELSLSNCAVVSEKDYQSGQHVIVRTSPNHKYIFTLRTHPSVVPGSVAFSLPQRKWAGLSIGQEIEVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKMAAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMDP------------QKIEVGLVVGNSQVAFEKAENSSLNLIGKAKT 201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      |  -       170       180       190       200 
                                                                                                                                                                                      157          170                               


Chain B from PDB  Type:PROTEIN  Length:189
 aligned with NSF_CRIGR | P18708 from UniProtKB/Swiss-Prot  Length:744

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
            NSF_CRIGR     1 MAGRSMQAARCPTDELSLSNCAVVSEKDYQSGQHVIVRTSPNHKYIFTLRTHPSVVPGSVAFSLPQRKWAGLSIGQEIEVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKMAAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMDPSILKGEPASGKRQKIEVGLVVGNSQVAFEKAENSSLNLIGKAKT 201
               SCOP domains d1qdnb1 B:1-85 N-terminal domain of NSF-N, NSF-Nn                                    d1qdnb2 B:86-201 C-terminal domain of NSF-N, NSF-Nc                                                                  SCOP domains
               CATH domains 1qdnB01 B:1-83  [code=2.40.40.20, no name defined]                                 1qdnB02 B:84-200  [code=3.10.330.10, no name defined]                                                                - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhhhh.eee.........eeeeeee..eeeeeeeee.......eeeehhhhhhhh......eeeeeee...hhhh...eeeeeeee.........eeehhhhhhhhhhhhh..eee...eeeeee..eeeeeeeeeee....------------....eee.....eeeeee......eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qdn B   1 MAGRSMQAARCPTDELSLSNCAVVSEKDYQSGQHVIVRTSPNHKYIFTLRTHPSVVPGSVAFSLPQRKWAGLSIGQEIEVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKMAAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMDP------------QKIEVGLVVGNSQVAFEKAENSSLNLIGKAKT 201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      |  -       170       180       190       200 
                                                                                                                                                                                      157          170                               


Chain C from PDB  Type:PROTEIN  Length:190
 aligned with NSF_CRIGR | P18708 from UniProtKB/Swiss-Prot  Length:744

    Alignment length:202
                             1                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199  
            NSF_CRIGR     - -MAGRSMQAARCPTDELSLSNCAVVSEKDYQSGQHVIVRTSPNHKYIFTLRTHPSVVPGSVAFSLPQRKWAGLSIGQEIEVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKMAAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMDPSILKGEPASGKRQKIEVGLVVGNSQVAFEKAENSSLNLIGKAKT 201
               SCOP domains -d1qdnc1 C:1-85 N-terminal domain of NSF-N, NSF-Nn                                    d1qdnc2 C:86-201 C-terminal domain of NSF-N, NSF-Nc                                                                  SCOP domains
               CATH domains -1qdnC01 C:1-83  [code=2.40.40.20, no name defined]                                 1qdnC02 C:84-200  [code=3.10.330.10, no name defined]                                                                - CATH domains
           Pfam domains (1) -----CDC48_N-1qdnC04 C:5-86                                                            ------------------------CDC48_2-1qdnC01 C:111-189                                                      ------------ Pfam domains (1)
           Pfam domains (2) -----CDC48_N-1qdnC05 C:5-86                                                            ------------------------CDC48_2-1qdnC02 C:111-189                                                      ------------ Pfam domains (2)
           Pfam domains (3) -----CDC48_N-1qdnC06 C:5-86                                                            ------------------------CDC48_2-1qdnC03 C:111-189                                                      ------------ Pfam domains (3)
         Sec.struct. author ....eeeeeee...hhhhhhh.eee.........eeeeeee..eeeeeeeee.......eeeehhhhhhhh......eeeeeee...hhhh...eeeeeeee.........eeehhhhhhhhhhhhh..eee...eeeeee..eeeeeeeeeee....------------....eee.....eeeeee......eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qdn C  -1 TMAGRSMQAARCPTDELSLSNCAVVSEKDYQSGQHVIVRTSPNHKYIFTLRTHPSVVPGSVAFSLPQRKWAGLSIGQEIEVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKMAAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMDP------------QKIEVGLVVGNSQVAFEKAENSSLNLIGKAKT 201
                            ||       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       | -         -|      179       189       199  
                           -1|                                                                                                                                                         157          170                               
                             1
   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  (2, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 6)

Asymmetric Unit
(-)
Clan: Cdc48_2-like (11)
(-)
Clan: no clan defined [family: CDC48_N] (7)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (NSF_CRIGR | P18708)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030496    midbody    A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NSF_CRIGR | P18708: 1d2n 1nsf 1qcs 3j94 3j95 3j96 3j97 3j98 3j99

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QDN)