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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF HUMAN CHROMOBOX HOMOLOG 3 (CBX3) WITH PEPTIDE
 
Authors :  M. F. Amaya, M. Ravichandran, P. Loppnau, I. Kozieradzki, A. M. Edwards C. H. Arrowsmith, J. Weigelt, C. Bountra, A. Bochkarev, J. Min, H. Ouya Structural Genomics Consortium (Sgc)
Date :  30 Jun 08  (Deposition) - 19 Aug 08  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Biol. Unit 5:  A,B,C,D,E,F,G,H  (1x)
Keywords :  Chromobox Homolog 3, Structural Genomics, Structural Genomics Consortium, Sgc, Chromatin Regulator, Nucleus, Phosphoprotein, Repressor, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Ruan, H. Ouyang, M. F. Amaya, M. Ravichandran, P. Loppnau, J. Min, J. Zang
Structural Basis Of The Chromodomain Of Cbx3 Bound To Methylated Peptides From Histone H1 And G9A.
Plos One V. 7 35376 2012
PubMed-ID: 22514736  |  Reference-DOI: 10.1371/JOURNAL.PONE.0035376

(-) Compounds

Molecule 1 - CHROMOBOX PROTEIN HOMOLOG 3
    ChainsA, C, E, G
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCHROMO 1 DOMAIN: RESIDUES 29-86
    GeneCBX3
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHETEROCHROMATIN PROTEIN 1 HOMOLOG GAMMA, HP1 GAMMA, MODIFIER 2 PROTEIN, HECH
 
Molecule 2 - HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 3
    ChainsB, D, F, H
    EngineeredYES
    FragmentUNP RESIDUES 179-190
    Other DetailsSYNTHETIC PEPTIDE WITH THE SEQUENCE MATCHING THE RESIDUES 179-190 OF THE HUMAN HISTONE H3-K9 METHYLTRANSFERASE 3, EHMT2_HUMAN, UNP ENTRY Q96KQ7
    SynonymHISTONE H3-K9 METHYLTRANSFERASE 3, H3-K9-HMTASE 3, EUCHROMATIC HISTONE-LYSINE N-METHYLTRANSFERASE 2, HLA-B-ASSOCIATED TRANSCRIPT 8, PROTEIN G9A, LYSINE N-METHYLTRANSFERASE 1C
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)AB      
Biological Unit 2 (1x)  CD    
Biological Unit 3 (1x)    EF  
Biological Unit 4 (1x)      GH
Biological Unit 5 (1x)ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1M3L4Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 5 (1, 4)
No.NameCountTypeFull Name
1M3L4Mod. Amino AcidN-TRIMETHYLLYSINE

(-) Sites  (0, 0)

(no "Site" information available for 3DM1)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:69 -C:69
2E:69 -G:69

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DM1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DM1)

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX3_HUMAN30-88
 
 
 
121-179
  4A:30-80
C:30-80
E:30-81
G:30-81
-
2CHROMO_1PS00598 Chromo domain signature.CBX3_HUMAN47-67
 
 
 
  4A:47-67
C:47-67
E:47-67
G:47-67
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX3_HUMAN30-88
 
 
 
121-179
  1A:30-80
-
-
-
-
2CHROMO_1PS00598 Chromo domain signature.CBX3_HUMAN47-67
 
 
 
  1A:47-67
-
-
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX3_HUMAN30-88
 
 
 
121-179
  1-
C:30-80
-
-
-
2CHROMO_1PS00598 Chromo domain signature.CBX3_HUMAN47-67
 
 
 
  1-
C:47-67
-
-
Biological Unit 3 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX3_HUMAN30-88
 
 
 
121-179
  1-
-
E:30-81
-
-
2CHROMO_1PS00598 Chromo domain signature.CBX3_HUMAN47-67
 
 
 
  1-
-
E:47-67
-
Biological Unit 4 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX3_HUMAN30-88
 
 
 
121-179
  1-
-
-
G:30-81
-
2CHROMO_1PS00598 Chromo domain signature.CBX3_HUMAN47-67
 
 
 
  1-
-
-
G:47-67
Biological Unit 5 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX3_HUMAN30-88
 
 
 
121-179
  4A:30-80
C:30-80
E:30-81
G:30-81
-
2CHROMO_1PS00598 Chromo domain signature.CBX3_HUMAN47-67
 
 
 
  4A:47-67
C:47-67
E:47-67
G:47-67

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.62bENST0000038337362bENSE00001868068HSCHR6_MHC_QBL:31855870-3185580764EHMT2_HUMAN1-14140--
1.64eENST0000038337364eENSE00001706010HSCHR6_MHC_QBL:31855160-3185509467EHMT2_HUMAN15-37230--
1.65aENST0000038337365aENSE00001599572HSCHR6_MHC_QBL:31854995-31854777219EHMT2_HUMAN37-110740--
1.65eENST0000038337365eENSE00001775009HSCHR6_MHC_QBL:31854687-31854434254EHMT2_HUMAN110-194854B:159-166
D:160-169
F:159-167
H:159-165
8
10
9
7
1.68iENST0000038337368iENSE00001728907HSCHR6_MHC_QBL:31851081-3185099785EHMT2_HUMAN195-223290--
1.68jENST0000038337368jENSE00001788063HSCHR6_MHC_QBL:31850905-3185086541EHMT2_HUMAN223-236140--
1.68mENST0000038337368mENSE00001596027HSCHR6_MHC_QBL:31850733-31850578156EHMT2_HUMAN237-288520--
1.72fENST0000038337372fENSE00001688918HSCHR6_MHC_QBL:31847773-31847639135EHMT2_HUMAN289-333450--
1.73ENST0000038337373ENSE00001675787HSCHR6_MHC_QBL:31847513-31847399115EHMT2_HUMAN334-372390--
1.74aENST0000038337374aENSE00001783494HSCHR6_MHC_QBL:31847241-31847140102EHMT2_HUMAN372-406350--
1.74eENST0000038337374eENSE00001756695HSCHR6_MHC_QBL:31846918-31846770149EHMT2_HUMAN406-455500--
1.74gENST0000038337374gENSE00001659464HSCHR6_MHC_QBL:31846677-31846534144EHMT2_HUMAN456-503480--
1.75dENST0000038337375dENSE00001776567HSCHR6_MHC_QBL:31846447-31846212236EHMT2_HUMAN504-582790--
1.75eENST0000038337375eENSE00001616295HSCHR6_MHC_QBL:31846132-31845950183EHMT2_HUMAN582-643620--
1.75fENST0000038337375fENSE00001626945HSCHR6_MHC_QBL:31845830-3184574883EHMT2_HUMAN643-671290--
1.76bENST0000038337376bENSE00001661306HSCHR6_MHC_QBL:31845272-31845166107EHMT2_HUMAN671-706360--
1.76dENST0000038337376dENSE00001674057HSCHR6_MHC_QBL:31845068-31844946123EHMT2_HUMAN707-747410--
1.77bENST0000038337377bENSE00001779819HSCHR6_MHC_QBL:31844853-31844752102EHMT2_HUMAN748-781340--
1.78kENST0000038337378kENSE00001761048HSCHR6_MHC_QBL:31843187-31843083105EHMT2_HUMAN782-816350--
1.78qENST0000038337378qENSE00001617974HSCHR6_MHC_QBL:31842970-31842816155EHMT2_HUMAN817-868520--
1.78tENST0000038337378tENSE00001680216HSCHR6_MHC_QBL:31842730-31842563168EHMT2_HUMAN868-924570--
1.79hENST0000038337379hENSE00001760590HSCHR6_MHC_QBL:31842121-31841977145EHMT2_HUMAN924-972490--
1.80bENST0000038337380bENSE00001750625HSCHR6_MHC_QBL:31841610-3184153378EHMT2_HUMAN973-998260--
1.80cENST0000038337380cENSE00001653707HSCHR6_MHC_QBL:31841180-31841065116EHMT2_HUMAN999-1037390--
1.80dENST0000038337380dENSE00001641889HSCHR6_MHC_QBL:31840956-3184087087EHMT2_HUMAN1037-1066300--
1.83dENST0000038337383dENSE00001692473HSCHR6_MHC_QBL:31839264-3183918679EHMT2_HUMAN1066-1092270--
1.84bENST0000038337384bENSE00001740322HSCHR6_MHC_QBL:31839020-31838845176EHMT2_HUMAN1093-1151590--
1.86bENST0000038337386bENSE00001647961HSCHR6_MHC_QBL:31838436-31837931506EHMT2_HUMAN1151-1210600--

(-) 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:52
 aligned with CBX3_HUMAN | Q13185 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:52
                                    38        48        58        68        78  
           CBX3_HUMAN    29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQ  80
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains 3dm1A00 A:29-80  [code=2.40.50.40, no name defined]  CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee..eeeeeeee...hhhhheeee.hhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -CHROMO_2  PDB: A:30-80 UniProt: 30-88               PROSITE (1)
                PROSITE (2) ------------------CHROMO_1  PDB: A:47-6------------- PROSITE (2)
                 Transcript ---------------------------------------------------- Transcript
                 3dm1 A  29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQ  80
                                    38        48        58        68        78  

Chain B from PDB  Type:PROTEIN  Length:8
 aligned with EHMT2_HUMAN | Q96KQ7 from UniProtKB/Swiss-Prot  Length:1210

    Alignment length:8
          EHMT2_HUMAN   179 KVHRARKT 186
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ...ee... Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
               Transcript 1 1.65e    Transcript 1
                 3dm1 B 159 KVHRARkT 166
                                  | 
                                165-M3L

Chain C from PDB  Type:PROTEIN  Length:52
 aligned with CBX3_HUMAN | Q13185 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:52
                                    38        48        58        68        78  
           CBX3_HUMAN    29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQ  80
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains 3dm1C00 C:29-80  [code=2.40.50.40, no name defined]  CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..eeeeeeee...hhhhheeee.hhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -CHROMO_2  PDB: C:30-80 UniProt: 30-88               PROSITE (1)
                PROSITE (2) ------------------CHROMO_1  PDB: C:47-6------------- PROSITE (2)
                 Transcript ---------------------------------------------------- Transcript
                 3dm1 C  29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQ  80
                                    38        48        58        68        78  

Chain D from PDB  Type:PROTEIN  Length:10
 aligned with EHMT2_HUMAN | Q96KQ7 from UniProtKB/Swiss-Prot  Length:1210

    Alignment length:10
                                   189
          EHMT2_HUMAN   180 VHRARKTMSK 189
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
               Transcript 1 Exon 1.65e Transcript 1
                 3dm1 D 160 VHRARkTMSK 169
                                 | 169
                                 |    
                               165-M3L

Chain E from PDB  Type:PROTEIN  Length:53
 aligned with CBX3_HUMAN | Q13185 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:53
                                    38        48        58        68        78   
           CBX3_HUMAN    29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQK  81
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains 3dm1E00 E:29-81  [code=2.40.50.40, no name defined]   CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee....eeeeeee.......eeeee.hhh.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -CHROMO_2  PDB: E:30-81 UniProt: 30-88                PROSITE (1)
                PROSITE (2) ------------------CHROMO_1  PDB: E:47-6-------------- PROSITE (2)
                 Transcript ----------------------------------------------------- Transcript
                 3dm1 E  29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQK  81
                                    38        48        58        68        78   

Chain F from PDB  Type:PROTEIN  Length:9
 aligned with EHMT2_HUMAN | Q96KQ7 from UniProtKB/Swiss-Prot  Length:1210

    Alignment length:9
          EHMT2_HUMAN   179 KVHRARKTM 187
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ...ee.... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
               Transcript 1 1.65e     Transcript 1
                 3dm1 F 159 KVHRARkTM 167
                                  |  
                                165-M3L

Chain G from PDB  Type:PROTEIN  Length:53
 aligned with CBX3_HUMAN | Q13185 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:53
                                    38        48        58        68        78   
           CBX3_HUMAN    29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQK  81
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains 3dm1G00 G:29-81  [code=2.40.50.40, no name defined]   CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee....eeeeeee...hhhhheeee.hhh.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -CHROMO_2  PDB: G:30-81 UniProt: 30-88                PROSITE (1)
                PROSITE (2) ------------------CHROMO_1  PDB: G:47-6-------------- PROSITE (2)
                 Transcript ----------------------------------------------------- Transcript
                 3dm1 G  29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQK  81
                                    38        48        58        68        78   

Chain H from PDB  Type:PROTEIN  Length:7
 aligned with EHMT2_HUMAN | Q96KQ7 from UniProtKB/Swiss-Prot  Length:1210

    Alignment length:7
          EHMT2_HUMAN   179 KVHRARK 185
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ...ee.. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
               Transcript 1 1.65e   Transcript 1
                 3dm1 H 159 KVHRARk 165
                                  |
                                165-M3L

   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 3DM1)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DM1)

(-) Gene Ontology  (48, 50)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E,G   (CBX3_HUMAN | Q13185)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:1990226    histone methyltransferase binding    Interacting selectively and non-covalently with a histone methyltransferase enzyme.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
biological process
    GO:0071549    cellular response to dexamethasone stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a dexamethasone stimulus.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000779    condensed chromosome, centromeric region    The region of a condensed chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0005719    nuclear euchromatin    The dispersed less dense form of chromatin in the interphase nucleus. It exists in at least two forms, a some being in the form of transcriptionally active chromatin which is the least condensed, while the rest is inactive euchromatin which is more condensed than active chromatin but less condensed than heterochromatin.
    GO:0005720    nuclear heterochromatin    A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
    GO:0005637    nuclear inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope.
    GO:0031618    nuclear pericentric heterochromatin    Nuclear heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.
    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.
    GO:0035985    senescence-associated heterochromatin focus    A transcriptionally-silent heterochromatin structure present in senescent cells. Contains the condensed chromatin of one chromosome and is enriched for histone modifications. Thought to repress expression of proliferation-promoting genes.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

Chain B,D,F,H   (EHMT2_HUMAN | Q96KQ7)
molecular function
    GO:0070742    C2H2 zinc finger domain binding    Interacting selectively and non-covalently with a C2H2-type zinc finger domain of a protein. The C2H2 zinc finger is the classical zinc finger domain, in which two conserved cysteines and histidines co-ordinate a zinc ion.
    GO:0046976    histone methyltransferase activity (H3-K27 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 27) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 27). This reaction is the addition of a methyl group onto lysine at position 27 of the histone H3 protein.
    GO:0046974    histone methyltransferase activity (H3-K9 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 9) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 9). This reaction is the addition of a methyl group onto lysine at position 9 of the histone H3 protein.
    GO:0018024    histone-lysine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    GO:1990841    promoter-specific chromatin binding    Interacting selectively and non-covalently with a section of chromatin that is associated with gene promoter sequences of DNA.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016279    protein-lysine N-methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue in a protein substrate.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006306    DNA methylation    The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
    GO:0009267    cellular response to starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nourishment.
    GO:0070734    histone H3-K27 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 27 of the histone.
    GO:0051567    histone H3-K9 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 9 of the histone.
    GO:0034968    histone lysine methylation    The modification of a histone by addition of one or more methyl groups to a lysine residue.
    GO:0016571    histone methylation    The modification of histones by addition of methyl groups.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    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:0018027    peptidyl-lysine dimethylation    The methylation of peptidyl-lysine to form peptidyl-N6,N6-dimethyl-L-lysine.
    GO:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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
        CBX3_HUMAN | Q131852l11 3kup 3tzd 5t1i
        EHMT2_HUMAN | Q96KQ72o8j 3k5k 3rjw 4nvq 5jhn 5jin 5jiy 5jj0 5t0k 5t0m 5ttf 5tuy 5vsc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3DM1)