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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MIXED LINEAGE KINASE MAP3K10 SH3 DOMAIN
 
Authors :  E. Ugochukwu, J. Eswaran, J. Elkins, T. Keates, A. C. W. Pike, G. Berridg P. Savitsky, M. Sundstrom, C. H. Arrowsmith, J. Weigelt, A. M. Edwards Delft, S. Knapp, Structural Genomics Consortium (Sgc)
Date :  27 Sep 07  (Deposition) - 23 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Map3K10, Mlk2, Sh3 Domain, Tkl Kinase, Mkn28, Structural Genomics, Structural Genomics Consortium, Sgc, Atp-Binding, Nucleotide- Binding, Phosphorylation, Serine/Threonine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Ugochukwu, J. Eswaran, J. Elkins, T. Keates, A. C. W. Pike, G. Berridge, P. Savitsky, M. Sundstrom, C. H. Arrowsmith, J. Weigelt, A. M. Edwards, F. Von Delft, S. Knapp
The Crystal Structure Of Human Mixed Lineage Kinase Map3K10 Sh3 Domain.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 10
    ChainsA, B, C, D
    EC Number2.7.11.25
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3) PHAGE RESISTANT ROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMAP3K10, MLK2, MST
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMIXED LINEAGE KINASE 2, PROTEIN KINASE MST

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (0, 0)

(no "Site" information available for 2RF0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RF0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RF0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RF0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RF0)

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002530551ENSE00001233426chr19:40697651-40698620970M3K10_HUMAN1-2282284A:17-78
B:17-78 (gaps)
C:17-78
D:18-78
62
62
62
61
1.2ENST000002530552ENSE00000706439chr19:40704282-40704462181M3K10_HUMAN228-288610--
1.3ENST000002530553ENSE00000706442chr19:40710392-40710540149M3K10_HUMAN288-338510--
1.4ENST000002530554ENSE00000706444chr19:40711028-40711203176M3K10_HUMAN338-396590--
1.5ENST000002530555ENSE00000706446chr19:40711818-40712064247M3K10_HUMAN397-479830--
1.6ENST000002530556ENSE00000706448chr19:40715010-40715126117M3K10_HUMAN479-518400--
1.7ENST000002530557ENSE00000706450chr19:40718712-40718883172M3K10_HUMAN518-575580--
1.8ENST000002530558ENSE00001197746chr19:40718983-40719095113M3K10_HUMAN575-613390--
1.9ENST000002530559ENSE00000706462chr19:40719424-40720128705M3K10_HUMAN613-8482360--
1.10ENST0000025305510ENSE00001139930chr19:40720877-40721481605M3K10_HUMAN848-9541070--

(-) 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:62
 aligned with M3K10_HUMAN | Q02779 from UniProtKB/Swiss-Prot  Length:954

    Alignment length:62
                                    26        36        46        56        66        76  
           M3K10_HUMAN   17 AGPVWTAVFDYEAAGDEELTLRRGDRVQVLSQDCAVSGDEGWWTGQLPSGRVGVFPSNYVAP 78
               SCOP domains d2rf0a_ A: automated matches                                   SCOP domains
               CATH domains 2rf0A00 A:17-78 SH3 Domains                                    CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..................eeeeee.hhhhhh...eeeee.....eeeee...ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:17-78 UniProt: 1-228 [INCOMPLETE]             Transcript 1
                  2rf0 A 17 AGPVWTAVFDYEAAGDEELTLRRGDRVQVLSQDCAVSGDEGWWTGQLPSGRVGVFPSNYVAP 78
                                    26        36        46        56        66        76  

Chain B from PDB  Type:PROTEIN  Length:56
 aligned with M3K10_HUMAN | Q02779 from UniProtKB/Swiss-Prot  Length:954

    Alignment length:62
                                    26        36        46        56        66        76  
           M3K10_HUMAN   17 AGPVWTAVFDYEAAGDEELTLRRGDRVQVLSQDCAVSGDEGWWTGQLPSGRVGVFPSNYVAP 78
               SCOP domains d2rf0b_ B: automated matches                                   SCOP domains
               CATH domains 2rf0B00 B:17-78 SH3 Domains                                    CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..................eeeeee..------..eeeee.....eeeee...ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:17-78 (gaps) UniProt: 1-228 [INCOMPLETE]      Transcript 1
                  2rf0 B 17 AGPVWTAVFDYEAAGDEELTLRRGDRVQVLSQD------EGWWTGQLPSGRVGVFPSNYVAP 78
                                    26        36        46  |     56        66        76  
                                                           49     56                      

Chain C from PDB  Type:PROTEIN  Length:62
 aligned with M3K10_HUMAN | Q02779 from UniProtKB/Swiss-Prot  Length:954

    Alignment length:62
                                    26        36        46        56        66        76  
           M3K10_HUMAN   17 AGPVWTAVFDYEAAGDEELTLRRGDRVQVLSQDCAVSGDEGWWTGQLPSGRVGVFPSNYVAP 78
               SCOP domains d2rf0c_ C: automated matches                                   SCOP domains
               CATH domains 2rf0C00 C:17-78 SH3 Domains                                    CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..................eeeeee.hhhhhh...eeeee.....eeeee...ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:17-78 UniProt: 1-228 [INCOMPLETE]             Transcript 1
                  2rf0 C 17 AGPVWTAVFDYEAAGDEELTLRRGDRVQVLSQDCAVSGDEGWWTGQLPSGRVGVFPSNYVAP 78
                                    26        36        46        56        66        76  

Chain D from PDB  Type:PROTEIN  Length:61
 aligned with M3K10_HUMAN | Q02779 from UniProtKB/Swiss-Prot  Length:954

    Alignment length:61
                                    27        37        47        57        67        77 
           M3K10_HUMAN   18 GPVWTAVFDYEAAGDEELTLRRGDRVQVLSQDCAVSGDEGWWTGQLPSGRVGVFPSNYVAP 78
               SCOP domains d2rf0d_ D: automated matches                                  SCOP domains
               CATH domains 2rf0D00 D:18-78 SH3 Domains                                   CATH domains
           Pfam domains (1) ---SH3_2-2rf0D01 D:21-78                                      Pfam domains (1)
           Pfam domains (2) ---SH3_2-2rf0D02 D:21-78                                      Pfam domains (2)
           Pfam domains (3) ---SH3_2-2rf0D03 D:21-78                                      Pfam domains (3)
           Pfam domains (4) ---SH3_2-2rf0D04 D:21-78                                      Pfam domains (4)
         Sec.struct. author ..eeee..................eeeeee.hhhhhh...eeeee.....eeeee...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:18-78 UniProt: 1-228 [INCOMPLETE]            Transcript 1
                  2rf0 D 18 GPVWTAVFDYEAAGDEELTLRRGDRVQVLSQDCAVSGDEGWWTGQLPSGRVGVFPSNYVAP 78
                                    27        37        47        57        67        77 

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: SH3 (175)

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (M3K10_HUMAN | Q02779)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004706    JUN kinase kinase kinase activity    Catalysis of the reaction: JNKK + ATP = JNKK phosphate + ADP. This reaction is the phosphorylation and activation of JUN kinase kinases (JNKKs).
    GO:0004709    MAP kinase kinase kinase activity    Catalysis of the phosphorylation and activation of a MAP kinase kinase; each MAP kinase kinase can be phosphorylated by any of several MAP kinase kinase kinases.
    GO:0043425    bHLH transcription factor binding    Interacting selectively and non-covalently with any of the basic Helix-Loop-Helix (bHLH) superfamily of transcription factors, important regulatory components in transcriptional networks of many developmental pathways.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0007254    JNK cascade    An intracellular protein kinase cascade containing at least a JNK (a MAPK), a JNKK (a MAPKK) and a JUN3K (a MAP3K). The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0007256    activation of JNKK activity    The initiation of the activity of the inactive enzyme JUN kinase kinase (JNKK) activity. JNKKs are involved in a signaling pathway that is primarily activated by cytokines and exposure to environmental stress.
    GO:0007257    activation of JUN kinase activity    The initiation of the activity of the inactive enzyme JUN kinase (JNK).
    GO:0000186    activation of MAPKK activity    The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK).
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0008219    cell death    Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
    GO:0043433    negative regulation of sequence-specific DNA binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    GO:0018107    peptidyl-threonine phosphorylation    The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0046330    positive regulation of JNK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade.
    GO:0043507    positive regulation of JUN kinase activity    Any process that activates or increases the frequency, rate or extent of JUN kinase activity.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007224    smoothened signaling pathway    A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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(-) Related Entries Specified in the PDB File

1fmk CRYSTAL STRUCTURE OF HUMAN TYROSINE-PROTEIN KINASE C-SRC
1oeb MONA/GADS SH3C DOMAIN