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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF THE DIMERIC BMP ANTAGONIST NBL1
 
Authors :  T. B. Thompson, K. Nolan, C. Kattamuri
Date :  24 Nov 14  (Deposition) - 14 Jan 15  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bmp Antagonist, Dan Family, Cystine-Knot, Bmp Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Nolan, C. Kattamuri, D. M. Luedeke, E. B. Angerman, S. A. Rankin, M. L. Stevens, A. M. Zorn, T. B. Thompson
Structure Of Neuroblastoma Suppressor Of Tumorigenicity 1 (Nbl1): Insights For The Functional Variability Across Bone Morphogenetic Protein (Bmp) Antagonists.
J. Biol. Chem. V. 290 4759 2015
PubMed-ID: 25561725  |  Reference-DOI: 10.1074/JBC.M114.628412

(-) Compounds

Molecule 1 - NEUROBLASTOMA SUPPRESSOR OF TUMORIGENICITY 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 52-167
    Gene: NBL1, DAN, DAND1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DAN DOMAIN FAMILY MEMBER 1,PROTEIN N03,ZINC FINGER PROTEIN DAN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:39 , ARG A:57binding site for Mono-Saccharide NAG A 501 bound to ASN A 39
2AC2SOFTWAREASN B:39binding site for Mono-Saccharide NAG B 501 bound to ASN B 39

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:35 -A:85
2A:49 -A:99
3A:59 -A:118
4A:63 -A:120
5A:82 -A:123
6B:35 -B:85
7B:49 -B:99
8B:59 -B:118
9B:63 -B:120
10B:82 -B:123

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:45 -His A:46
2Cys A:99 -Pro A:100

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X1J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X1J)

(-) Exons   (0, 0)

(no "Exon" information available for 4X1J)

(-) 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:83
                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee.........eeeeeeeeeeeeeee...ee.eeeeeeeeeeeeeeee......eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 4x1j A  30 DKSAWCEAKNITQIVGHSGCEAKSIQNRACLGQCFSYSVPNTFVHCDSCMPAQSMWEIVTLECPGVDKLVEKILHCSCQACGK 125
                                    39        49        59        69  ||    86        96    || 112       122   
                                                                     72|                  101|                 
                                                                      80                   108                 


Chain B from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee.......eeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeee........eeeeeeeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 4x1j B  30 DKSAWCEAKNITQIVGHSGCEAKSIQNRACLGQCFSYSVPESLVHCDSCMPAQSMWEIVTLECPGHEEVPRVDKLVEKILHCSCQACGKEPSHE 130
                                    39        49        59        69|       86        96       106       116       126    
                                                                  69|                                                     
                                                                   77
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  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 4X1J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X1J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X1J)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  NBL1_HUMAN | P41271
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 Related Entries

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

UniProtKB/Swiss-Prot
        NBL1_HUMAN | P41271: 4yu8

(-) Related Entries Specified in the PDB File

4jph THE RELATED ENTRY IS A PROTEIN THAT IS A PART OF THE SAME PROTEIN FAMILY.