Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE LMO2:LDB1-LID COMPLEX, C2 CRYSTAL FORM
 
Authors :  K. El Omari, D. Karia, C. Porcher, E. J. Mancini
Date :  06 Jul 10  (Deposition) - 21 Jul 10  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,I,J,K,L,M
Biol. Unit 1:  A,I  (1x)
Biol. Unit 2:  D,L  (1x)
Biol. Unit 3:  E,M  (1x)
Biol. Unit 4:  B,J  (1x)
Biol. Unit 5:  C,K  (1x)
Keywords :  Oncoprotein, T-Cell Leukemia, Proto-Oncogene, Transcription, Developmental Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. El Omari, S. J. Hoosdally, K. Tuladhar, D. Karia, P. Vyas, R. Patient, C. Porcher, E. J. Mancini
Structure Of The Leukemia Oncogene Lmo2: Implications For The Assembly Of A Hematopoietic Transcription Factor Complex.
Blood V. 117 2146 2011
PubMed-ID: 21076045  |  Reference-DOI: 10.1182/BLOOD-2010-07-293357

(-) Compounds

Molecule 1 - RHOMBOTIN-2
    ChainsA, B, C, D, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 26-156
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLIM DOMAIN ONLY PROTEIN 2, CYSTEINE-RICH PROTEIN TTG-2, T- CELL TRANSLOCATION PROTEIN 2, LMO-2
 
Molecule 2 - LIM DOMAIN-BINDING PROTEIN 1
    ChainsI, J, K, L, M
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 334-368
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNUCLEAR LIM INTERACTOR, CARBOXYL-TERMINAL LIM DOMAIN-BINDING PROTEIN 2, LIM DOMAIN-BINDING FACTOR CLIM2, LDB-1, CLIM-2, HLDB1

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit ABCDEIJKLM
Biological Unit 1 (1x)A    I    
Biological Unit 2 (1x)   D    L 
Biological Unit 3 (1x)    E    M
Biological Unit 4 (1x) B    J   
Biological Unit 5 (1x)  C    K  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 22)

Asymmetric Unit (2, 22)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2ZN20Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:115 , CYS A:118 , CYS A:137 , ASP A:140BINDING SITE FOR RESIDUE ZN A 201
02AC2SOFTWARECYS A:87 , CYS A:90 , HIS A:109 , CYS A:112BINDING SITE FOR RESIDUE ZN A 202
03AC3SOFTWARECYS A:50 , CYS A:53 , CYS A:73 , ASP A:76BINDING SITE FOR RESIDUE ZN A 203
04AC4SOFTWARECYS A:26 , HIS A:44 , CYS A:47BINDING SITE FOR RESIDUE ZN A 204
05AC5SOFTWARECYS B:115 , CYS B:118 , CYS B:137 , ASP B:140BINDING SITE FOR RESIDUE ZN B 201
06AC6SOFTWARECYS B:87 , CYS B:90 , HIS B:109 , CYS B:112BINDING SITE FOR RESIDUE ZN B 202
07AC7SOFTWARECYS B:50 , CYS B:53 , CYS B:73 , ASP B:76BINDING SITE FOR RESIDUE ZN B 203
08AC8SOFTWARECYS B:23 , CYS B:26 , HIS B:44 , CYS B:47BINDING SITE FOR RESIDUE ZN B 204
09AC9SOFTWARECYS C:115 , CYS C:118 , CYS C:137 , ASP C:140BINDING SITE FOR RESIDUE ZN C 201
10BC1SOFTWARECYS C:87 , CYS C:90 , HIS C:109 , CYS C:112BINDING SITE FOR RESIDUE ZN C 202
11BC2SOFTWARECYS C:50 , CYS C:53 , CYS C:73 , ASP C:76BINDING SITE FOR RESIDUE ZN C 203
12BC3SOFTWARECYS C:26 , HIS C:44 , CYS C:47BINDING SITE FOR RESIDUE ZN C 204
13BC4SOFTWARECYS D:115 , CYS D:118 , CYS D:137 , ASP D:140BINDING SITE FOR RESIDUE ZN D 201
14BC5SOFTWARECYS D:87 , CYS D:90 , HIS D:109 , CYS D:112BINDING SITE FOR RESIDUE ZN D 202
15BC6SOFTWARECYS D:50 , CYS D:53 , CYS D:73 , ASP D:76BINDING SITE FOR RESIDUE ZN D 203
16BC7SOFTWARECYS D:23 , CYS D:26 , HIS D:44 , CYS D:47BINDING SITE FOR RESIDUE ZN D 204
17BC8SOFTWARECYS E:115 , CYS E:118 , CYS E:137 , ASP E:140BINDING SITE FOR RESIDUE ZN E 201
18BC9SOFTWARECYS E:87 , CYS E:90 , HIS E:109 , CYS E:112BINDING SITE FOR RESIDUE ZN E 202
19CC1SOFTWARECYS E:50 , CYS E:53 , CYS E:73 , ASP E:76BINDING SITE FOR RESIDUE ZN E 203
20CC2SOFTWARECYS E:23 , CYS E:26 , HIS E:44 , CYS E:47BINDING SITE FOR RESIDUE ZN E 204
21CC3SOFTWAREARG C:74 , LEU D:68BINDING SITE FOR RESIDUE CL D 1148
22CC4SOFTWAREARG B:70BINDING SITE FOR RESIDUE CL B 1149

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 14)

Asymmetric Unit (2, 14)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIM_DOMAIN_2PS50023 LIM domain profile.RBTN2_HUMAN28-90
92-154
 
 
 
 
  6D:21-83
A:85-147
B:85-147
C:85-147
D:85-147
E:85-147
2LIM_DOMAIN_1PS00478 LIM zinc-binding domain signature.RBTN2_HUMAN30-64
 
 
94-129
 
 
 
 
  8B:23-57
D:23-57
E:23-57
A:87-122
B:87-122
C:87-122
D:87-122
E:87-122
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIM_DOMAIN_2PS50023 LIM domain profile.RBTN2_HUMAN28-90
92-154
 
 
 
 
  1-
A:85-147
-
-
-
-
2LIM_DOMAIN_1PS00478 LIM zinc-binding domain signature.RBTN2_HUMAN30-64
 
 
94-129
 
 
 
 
  1-
-
-
A:87-122
-
-
-
-
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIM_DOMAIN_2PS50023 LIM domain profile.RBTN2_HUMAN28-90
92-154
 
 
 
 
  2D:21-83
-
-
-
D:85-147
-
2LIM_DOMAIN_1PS00478 LIM zinc-binding domain signature.RBTN2_HUMAN30-64
 
 
94-129
 
 
 
 
  2-
D:23-57
-
-
-
-
D:87-122
-
Biological Unit 3 (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIM_DOMAIN_2PS50023 LIM domain profile.RBTN2_HUMAN28-90
92-154
 
 
 
 
  1-
-
-
-
-
E:85-147
2LIM_DOMAIN_1PS00478 LIM zinc-binding domain signature.RBTN2_HUMAN30-64
 
 
94-129
 
 
 
 
  2-
-
E:23-57
-
-
-
-
E:87-122
Biological Unit 4 (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIM_DOMAIN_2PS50023 LIM domain profile.RBTN2_HUMAN28-90
92-154
 
 
 
 
  1-
-
B:85-147
-
-
-
2LIM_DOMAIN_1PS00478 LIM zinc-binding domain signature.RBTN2_HUMAN30-64
 
 
94-129
 
 
 
 
  2B:23-57
-
-
-
B:87-122
-
-
-
Biological Unit 5 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIM_DOMAIN_2PS50023 LIM domain profile.RBTN2_HUMAN28-90
92-154
 
 
 
 
  1-
-
-
C:85-147
-
-
2LIM_DOMAIN_1PS00478 LIM zinc-binding domain signature.RBTN2_HUMAN30-64
 
 
94-129
 
 
 
 
  1-
-
-
-
-
C:87-122
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 2XJZ)

(-) 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:125
 aligned with RBTN2_HUMAN | P25791 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:125
                                    41        51        61        71        81        91       101       111       121       131       141       151     
          RBTN2_HUMAN    32 GCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKING 156
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee..eee...................eeeee..eeehhhhhhhhhh..ee......ee....eeeee..eeee.hhh.............eeeee..eeee..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LIM_DOMAIN_2  PDB: - UniProt: 28-90                        -LIM_DOMAIN_2  PDB: A:85-147 UniProt: 92-154                    -- PROSITE (1)
                PROSITE (2) LIM_DOMAIN_1  PDB: -             -----------------------------LIM_DOMAIN_1  PDB: A:87-122         --------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xjz A  25 GCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKING 149
                                    34        44        54        64        74        84        94       104       114       124       134       144     

Chain B from PDB  Type:PROTEIN  Length:122
 aligned with RBTN2_HUMAN | P25791 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:126
                                    39        49        59        69        79        89        99       109       119       129       139       149      
          RBTN2_HUMAN    30 CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKIN 155
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeee..eee..............----..eeee..eeehhhhhhhhhh..ee......ee....eeeee..eeee.hhh.............eeeee..eeee..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) LIM_DOMAIN_2  PDB: - UniProt: 28-90                          -LIM_DOMAIN_2  PDB: B:85-147 UniProt: 92-154                    - PROSITE (1)
                PROSITE (2) LIM_DOMAIN_1  PDB: B:23-57         -----------------------------LIM_DOMAIN_1  PDB: B:87-122         -------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xjz B  23 CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRL----RRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKIN 148
                                    32        42        52    |   62        72        82        92       102       112       122       132       142      
                                                             57   62                                                                                      

Chain C from PDB  Type:PROTEIN  Length:112
 aligned with RBTN2_HUMAN | P25791 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:125
                                    40        50        60        70        80        90       100       110       120       130       140       150     
          RBTN2_HUMAN    31 GGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKIN 155
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....-------------........................eee..eeehhhhhhhhhh..ee......ee....eeeee..eeee.hhh.............eeeee..eeee..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LIM_DOMAIN_2  PDB: - UniProt: 28-90                         -LIM_DOMAIN_2  PDB: C:85-147 UniProt: 92-154                    - PROSITE (1)
                PROSITE (2) LIM_DOMAIN_1  PDB: -              -----------------------------LIM_DOMAIN_1  PDB: C:87-122         -------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xjz C  24 GGCQ-------------QYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKIN 148
                               |     -       |43        53        63        73        83        93       103       113       123       133       143     
                              27            41                                                                                                           

Chain D from PDB  Type:PROTEIN  Length:129
 aligned with RBTN2_HUMAN | P25791 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:129
                                    35        45        55        65        75        85        95       105       115       125       135       145         
          RBTN2_HUMAN    26 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKI 154
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeee..eeee..................eeeee..eeehhhhhhhhhh..ee......ee....eeeee..eeee.hhh.............eeeee..eeee..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --LIM_DOMAIN_2  PDB: D:21-83 UniProt: 28-90                      -LIM_DOMAIN_2  PDB: D:85-147 UniProt: 92-154                     PROSITE (1)
                PROSITE (2) ----LIM_DOMAIN_1  PDB: D:23-57         -----------------------------LIM_DOMAIN_1  PDB: D:87-122         ------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xjz D  19 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKI 147
                                    28        38        48        58        68        78        88        98       108       118       128       138         

Chain E from PDB  Type:PROTEIN  Length:127
 aligned with RBTN2_HUMAN | P25791 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:127
                                    39        49        59        69        79        89        99       109       119       129       139       149       
          RBTN2_HUMAN    30 CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKING 156
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------LIM-2xjzE01 E:87-145                                       ---- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------LIM-2xjzE02 E:87-145                                       ---- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------LIM-2xjzE03 E:87-145                                       ---- Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------LIM-2xjzE04 E:87-145                                       ---- Pfam domains (4)
           Pfam domains (5) ----------------------------------------------------------------LIM-2xjzE05 E:87-145                                       ---- Pfam domains (5)
           Pfam domains (6) ----------------------------------------------------------------LIM-2xjzE06 E:87-145                                       ---- Pfam domains (6)
           Pfam domains (7) ----------------------------------------------------------------LIM-2xjzE07 E:87-145                                       ---- Pfam domains (7)
           Pfam domains (8) ----------------------------------------------------------------LIM-2xjzE08 E:87-145                                       ---- Pfam domains (8)
           Pfam domains (9) ----------------------------------------------------------------LIM-2xjzE09 E:87-145                                       ---- Pfam domains (9)
          Pfam domains (10) ----------------------------------------------------------------LIM-2xjzE10 E:87-145                                       ---- Pfam domains (10)
         Sec.struct. author ............eeee..eee...................eeeee..eeehhhhhhhhhh..ee......ee....eeeee..eeee.hhh.............eeeee..eeee...hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LIM_DOMAIN_2  PDB: - UniProt: 28-90                          -LIM_DOMAIN_2  PDB: E:85-147 UniProt: 92-154                    -- PROSITE (1)
                PROSITE (2) LIM_DOMAIN_1  PDB: E:23-57         -----------------------------LIM_DOMAIN_1  PDB: E:87-122         --------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xjz E  23 CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKING 149
                                    32        42        52        62        72        82        92       102       112       122       132       142       

Chain I from PDB  Type:PROTEIN  Length:29
 aligned with LDB1_HUMAN | Q86U70 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:29
                                   345       355         
           LDB1_HUMAN   336 DVMVVGEPTLMGGEFGDEDERLITRLENT 364
               SCOP domains ----------------------------- SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author .eee....ee.hhh.....eee.eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ----------------------------- PROSITE
                 Transcript ----------------------------- Transcript
                 2xjz I 336 DVMVVGEPTLMGGEFGDEDERLITRLENT 364
                                   345       355         

Chain J from PDB  Type:PROTEIN  Length:31
 aligned with LDB1_HUMAN | Q86U70 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:31
                                   342       352       362 
           LDB1_HUMAN   333 QVPDVMVVGEPTLMGGEFGDEDERLITRLEN 363
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author ...eeee....ee.hhhh....ee..eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                 2xjz J 333 SVPDVMVVGEPTLMGGEFGDEDERLITRLEN 363
                                   342       352       362 

Chain K from PDB  Type:PROTEIN  Length:21
 aligned with LDB1_HUMAN | Q86U70 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:21
                                   345       355 
           LDB1_HUMAN   336 DVMVVGEPTLMGGEFGDEDER 356
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author .eee....ee.hhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                 2xjz K 336 DVMVVGEPTLMGGEFGDEDER 356
                                   345       355 

Chain L from PDB  Type:PROTEIN  Length:29
 aligned with LDB1_HUMAN | Q86U70 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:29
                                   345       355         
           LDB1_HUMAN   336 DVMVVGEPTLMGGEFGDEDERLITRLENT 364
               SCOP domains ----------------------------- SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author .eee....ee.hhhh....eee.eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ----------------------------- PROSITE
                 Transcript ----------------------------- Transcript
                 2xjz L 336 DVMVVGEPTLMGGEFGDEDERLITRLENT 364
                                   345       355         

Chain M from PDB  Type:PROTEIN  Length:26
 aligned with LDB1_HUMAN | Q86U70 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:26
                                   345       355      
           LDB1_HUMAN   336 DVMVVGEPTLMGGEFGDEDERLITRL 361
               SCOP domains -------------------------- SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author .eee....ee.hhh.....eee.eee Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                 2xjz M 336 DVMVVGEPTLMGGEFGDEDERLITRL 361
                                   345       355      

   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 2XJZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XJZ)

(-) Pfam Domains  (1, 10)

Asymmetric Unit
(-)
Family: LIM (23)
1aLIM-2xjzE01E:87-145
1bLIM-2xjzE02E:87-145
1cLIM-2xjzE03E:87-145
1dLIM-2xjzE04E:87-145
1eLIM-2xjzE05E:87-145
1fLIM-2xjzE06E:87-145
1gLIM-2xjzE07E:87-145
1hLIM-2xjzE08E:87-145
1iLIM-2xjzE09E:87-145
1jLIM-2xjzE10E:87-145

(-) Gene Ontology  (54, 60)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (RBTN2_HUMAN | P25791)
molecular function
    GO:0070888    E-box binding    Interacting selectively and non-covalently with an E-box, a DNA motif with the consensus sequence CANNTG that is found in the promoters of a wide array of genes expressed in neurons, muscle and other tissues.
    GO:0001102    RNA polymerase II activating transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    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: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:0048037    cofactor binding    Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0001190    transcriptional activator activity, RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
    GO:0001228    transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0097067    cellular response to thyroid hormone stimulus    A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a thyroid hormone stimulus.
    GO:0042789    mRNA transcription from RNA polymerase II promoter    The cellular synthesis of messenger RNA (mRNA) from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
cellular component
    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:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Chain I,J,K,L,M   (LDB1_HUMAN | Q86U70)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0030274    LIM domain binding    Interacting selectively and non-covalently with a LIM domain (for Lin-11 Isl-1 Mec-3) of a protein, a domain with seven conserved cysteine residues and a histidine, that binds two zinc ions and acts as an interface for protein-protein interactions.
    GO:0001102    RNA polymerase II activating transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0001158    enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
    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:0000989    transcription factor activity, transcription factor binding    Interacting selectively and non-covalently with a specific transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0009948    anterior/posterior axis specification    The establishment, maintenance and elaboration of the anterior/posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    GO:0022607    cellular component assembly    The aggregation, arrangement and bonding together of a cellular component.
    GO:0021702    cerebellar Purkinje cell differentiation    The process in which neuroblasts acquire specialized structural and/or functional features that characterize the mature cerebellar Purkinje cell. Differentiation includes the processes involved in commitment of a neuroblast to a Purkinje cell fate. A Purkinje cell is an inhibitory GABAergic neuron found in the cerebellar cortex that projects to the deep cerebellar nuclei and brain stem.
    GO:0021549    cerebellum development    The process whose specific outcome is the progression of the cerebellum over time, from its formation to the mature structure. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. In mice, the cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills.
    GO:0010669    epithelial structure maintenance    A tissue homeostatic process required for the maintenance of epithelial structure.
    GO:0001702    gastrulation with mouth forming second    A gastrulation process in which the initial invagination becomes the anus and the mouth forms second.
    GO:0001942    hair follicle development    The process whose specific outcome is the progression of the hair follicle over time, from its formation to the mature structure. A hair follicle is a tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open.
    GO:0060322    head development    The biological process whose specific outcome is the progression of a head from an initial condition to its mature state. The head is the anterior-most division of the body.
    GO:0043973    histone H3-K4 acetylation    The modification of histone H3 by the addition of an acetyl group to a lysine residue at position 4 of the histone.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0045647    negative regulation of erythrocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of erythrocyte differentiation.
    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:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    GO:0045785    positive regulation of cell adhesion    Any process that activates or increases the frequency, rate or extent of cell adhesion.
    GO:0046985    positive regulation of hemoglobin biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hemoglobin, an oxygen carrying, conjugated protein containing four heme groups and globin.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0032784    regulation of DNA-templated transcription, elongation    Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
    GO:0030334    regulation of cell migration    Any process that modulates the frequency, rate or extent of cell migration.
    GO:0051893    regulation of focal adhesion assembly    Any process that modulates the frequency, rate or extent of focal adhesion formation, the establishment and maturation of focal adhesions.
    GO:0043549    regulation of kinase activity    Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0035019    somatic stem cell population maintenance    Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0000972    transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery    The chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery. In S. cerevisiae, this process involves cis-acting DNA sequences such as the TATA box and upstream activating sequence (UAS) elements, trans-acting transcriptional activators, and also the 3'-UTR of the transcript.
cellular component
    GO:0031252    cell leading edge    The area of a motile cell closest to the direction of movement.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2xjz)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2xjz
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  LDB1_HUMAN | Q86U70
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  RBTN2_HUMAN | P25791
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  LDB1_HUMAN | Q86U70
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RBTN2_HUMAN | P25791
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LDB1_HUMAN | Q86U702xjy 2ypa
        RBTN2_HUMAN | P257912xjy 2ypa 4kfz

(-) Related Entries Specified in the PDB File

2xjy CRYSTAL STRUCTURE OF THE LMO2:LDB1-LID COMPLEX, P21 CRYSTAL FORM