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(-) Description

Title :  3D SOLUTION NMR STRUCTURE OF THE WILD TYPE HMG-BOX DOMAIN OF THE HUMAN MALE SEX DETERMINING FACTOR SRY COMPLEXED TO DNA
 
Authors :  G. M. Clore, E. C. Murphy
Date :  23 Jul 01  (Deposition) - 03 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C
Keywords :  Male Sex Determining Factor, Sry, Sex-Reversal Mutation, Dna Bending Mutant, Dipolar Couplings, Multidimensional Nmr, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. C. Murphy, V. B. Zhurkin, J. M. Louis, G. Cornilescu, G. M. Clore
Structural Basis For Sry-Dependent 46-X, Y Sex Reversal: Modulation Of Dna Bending By A Naturally Occurring Point Mutation.
J. Mol. Biol. V. 312 481 2001
PubMed-ID: 11563911  |  Reference-DOI: 10.1006/JMBI.2001.4977
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SEX-DETERMINING REGION Y PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET21A
    Fragment: HMG-BOX DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SRY
 
Molecule 2 - 5'-D(*CP*CP*TP*GP*CP*AP*CP*AP*AP*AP*CP*AP*CP*C)- 3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*GP*GP*TP*GP*TP*TP*TP*GP*TP*GP*CP*AP*GP*G)- 3'
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1J46)

(-) Sites  (0, 0)

(no "Site" information available for 1J46)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J46)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J46)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (25, 25)

NMR Structure (25, 25)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_003718V60ASRY_HUMANDisease (SRXY1)764249635AV5A
02UniProtVAR_003719V60LSRY_HUMANDisease (SRXY1)104894957AV5L
03UniProtVAR_003720R62GSRY_HUMANDisease (SRXY1)  ---AR7G
04UniProtVAR_003721M64ISRY_HUMANDisease (SRXY1)104894969AM9I
05UniProtVAR_017298M64RSRY_HUMANDisease (SRXY1)  ---AM9R
06UniProtVAR_017299F67VSRY_HUMANDisease (SRXY1)  ---AF12V
07UniProtVAR_003722I68TSRY_HUMANDisease (SRXY1)104894968AI13T
08UniProtVAR_078433R75MSRY_HUMANDisease (SRXY1)  ---AR20M
09UniProtVAR_017300R76SSRY_HUMANDisease (SRXY1)  ---AR21S
10UniProtVAR_003723M78TSRY_HUMANDisease (SRXY1)  ---AM23T
11UniProtVAR_017301N87YSRY_HUMANDisease (SRXY1)  ---AN32Y
12UniProtVAR_003724I90MSRY_HUMANDisease (SRXY1)104894959AI35M
13UniProtVAR_003725S91GSRY_HUMANDisease (SRXY1)  ---AS36G
14UniProtVAR_017302G95ESRY_HUMANDisease (SRXY1)104894972AG40E
15UniProtVAR_003726G95RSRY_HUMANDisease (SRXY1)104894974AG40R
16UniProtVAR_003727L101HSRY_HUMANDisease (SRXY1)  ---AL46H
17UniProtVAR_003728K106ISRY_HUMANDisease (SRXY1)104894964AK51I
18UniProtVAR_003729P108RSRY_HUMANDisease (SRXY1)  ---AP53R
19UniProtVAR_003730F109SSRY_HUMANDisease (SRXY1)104894956AF54S
20UniProtVAR_003731A113TSRY_HUMANDisease (SRXY1)104894966AA58T
21UniProtVAR_003732P125LSRY_HUMANDisease (SRXY1)  ---AP70L
22UniProtVAR_003733Y127CSRY_HUMANDisease (SRXY1)  ---AY72C
23UniProtVAR_017303Y127FSRY_HUMANDisease (SRXY1)104894973AY72F
24UniProtVAR_017304P131RSRY_HUMANDisease (SRXY1)  ---AP76R
25UniProtVAR_003734R133WSRY_HUMANDisease (SRXY1)104894976AR78W
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.SRY_HUMAN60-128  1A:5-73

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003830701ENSE00001494622Y:2655740-2654896845SRY_HUMAN1-2362361A:1-8585

(-) Sequences/Alignments

NMR Structure
   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:85
 aligned with SRY_HUMAN | Q05066 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:85
                                    65        75        85        95       105       115       125       135     
            SRY_HUMAN    56 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK 140
               SCOP domains d1j46a_ A: SRY                                                                        SCOP domains
               CATH domains 1j46A00 A:1-85 DNA Binding (I), subunit A                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
             SAPs(SNPs) (1) ----A-G-I--VT------MS-T--------Y--MG---E-----H----I-RS---T-----------L-C---R-W------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----L---R------------------------------R-------------------------------F------------- SAPs(SNPs) (2)
                    PROSITE ----HMG_BOX_2  PDB: A:5-73 UniProt: 60-128                               ------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-85 UniProt: 1-236 [INCOMPLETE]                                     Transcript 1
                 1j46 A   1 MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK  85
                                    10        20        30        40        50        60        70        80     


Chain B from PDB  Type:DNA  Length:14
                                              
                 1j46 B 101 CCTGCACAAACACC 114
                                   110    


Chain C from PDB  Type:DNA  Length:14
                                              
                 1j46 C 115 GGTGTTTGTGCAGG 128
                                   124
   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  (1, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J46)

(-) Gene Ontology  (24, 24)

NMR Structure(hide GO term definitions)
Chain A   (SRY_HUMAN | Q05066)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008301    DNA binding, bending    The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0003705    transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:0030238    male sex determination    The specification of male sex of an individual organism.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:2000020    positive regulation of male gonad development    Any process that activates or increases the frequency, rate or extent of male gonad development.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007530    sex determination    Any process that establishes and transmits the specification of sexual status of an individual organism.
    GO:0007548    sex differentiation    The establishment of the sex of an organism by physical differentiation.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    GO:0044798    nuclear transcription factor complex    A protein complex, located in the nucleus, that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SRY_HUMAN | Q05066: 1hry 1hrz 1j47 2gzk

(-) Related Entries Specified in the PDB File

1j47 M9I MUTANT OF THE HMG-BOX DOMAIN OF THE HUMAN MALE SEX DETERMINING FACTOR SRY COMPLEXED TO DNA