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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN HMG BOX-CONTAINING PROTEIN 1, HBP1
 
Authors :  A. Chaikuad, E. Krysztofinska, R. Cocking, M. Vollmar, W. W. Yue, T. Kro E. Ugochukwu, P. Filippakopoulos, F. Von Delft, C. H. Arrowsmith, J. A. M. Edwards, C. Bountra, U. Oppermann, Structural Genomics Conso
Date :  25 Feb 11  (Deposition) - 16 Mar 11  (Release) - 16 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Sgc, Hmg Box Transcription Factor 1, Hbp1, Axh Domain, Structural Genomics Consortium, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Chaikuad, E. Krysztofinska, R. Cocking, M. Vollmar, W. W. Yue, T. Krojer, E. Ugochukwu, P. Filippakopoulos, F. Von Delft, C. H. Arrowsmith, J. Weigelt, A. M. Edwards, C. Bountra, U. Oppermann, Structural Genomics Consortium
Crystal Structure Of Human Hmg Box-Containing Protein 1, Hbp1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HMG BOX-CONTAINING PROTEIN 1
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)-R3-PRARE2
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: AXH DOMAIN RESIDUES 206-342
    Gene: HBP1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HMG BOX TRANSCRIPTION FACTOR 1, HIGH MOBILITY GROUP BOX TRANSCRIPTION FACTOR 1

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 38)

Asymmetric Unit (2, 38)
No.NameCountTypeFull Name
1EDO35Ligand/Ion1,2-ETHANEDIOL
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 13)
No.NameCountTypeFull Name
1EDO12Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 17)
No.NameCountTypeFull Name
1EDO16Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 8)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION

(-) Sites  (38, 38)

Asymmetric Unit (38, 38)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH B:117 , HIS B:267 , HIS B:329 , ILE B:330 , HOH B:411BINDING SITE FOR RESIDUE SO4 B 1
02AC2SOFTWAREHIS A:267 , HIS A:329 , ILE A:330 , HOH A:361BINDING SITE FOR RESIDUE SO4 A 2
03AC3SOFTWAREHIS C:267 , HIS C:329 , ILE C:330 , HOH C:489BINDING SITE FOR RESIDUE SO4 C 3
04AC4SOFTWARETYR A:313 , PRO A:314 , SER A:315 , HOH A:376BINDING SITE FOR RESIDUE EDO A 343
05AC5SOFTWAREEDO B:27 , ARG B:220 , TRP B:231 , LYS B:279 , GLU B:295 , HOH B:372 , HOH B:373 , HOH B:374BINDING SITE FOR RESIDUE EDO B 3
06AC6SOFTWAREASP B:260 , GLY B:261 , LYS B:263 , PRO B:284BINDING SITE FOR RESIDUE EDO B 4
07AC7SOFTWAREEDO B:10 , GLU B:269 , SER B:270 , VAL B:271 , SER B:276BINDING SITE FOR RESIDUE EDO B 6
08AC8SOFTWAREEDO A:24 , ARG A:220 , TRP A:231 , LYS A:279 , GLU A:295 , HOH A:408 , HOH C:375BINDING SITE FOR RESIDUE EDO A 7
09AC9SOFTWARESER A:266 , GLU A:268 , LYS A:279 , THR A:281 , THR A:293 , EDO C:9 , LEU C:291BINDING SITE FOR RESIDUE EDO A 8
10BC1SOFTWAREEDO A:8 , HOH A:86 , HIS A:224 , THR A:281 , THR A:293 , EDO C:17 , HIS C:224 , THR C:281 , THR C:293BINDING SITE FOR RESIDUE EDO C 9
11BC2SOFTWAREEDO B:6 , EDO B:28 , HIS B:224 , LYS B:225 , SER B:270 , VAL B:271 , HOH B:356BINDING SITE FOR RESIDUE EDO B 10
12BC3SOFTWAREEDO A:23 , TRP C:231 , LYS C:279BINDING SITE FOR RESIDUE EDO C 11
13BC4SOFTWARELYS A:225 , GLY A:226 , HIS A:254 , ASP A:289 , HOH A:393BINDING SITE FOR RESIDUE EDO A 12
14BC5SOFTWAREASP A:260 , GLY A:261 , ASP A:283 , PRO A:284 , GLY A:285BINDING SITE FOR RESIDUE EDO A 13
15BC6SOFTWAREGLY B:256 , TYR B:257 , HOH B:477BINDING SITE FOR RESIDUE EDO B 16
16BC7SOFTWAREEDO C:9 , SER C:266 , HIS C:267 , GLU C:268 , LYS C:279 , LEU C:280 , THR C:281 , HOH C:423BINDING SITE FOR RESIDUE EDO C 17
17BC8SOFTWARECYS A:325 , HOH A:436 , HOH B:398BINDING SITE FOR RESIDUE EDO A 18
18BC9SOFTWAREEDO B:26 , HIS B:224 , THR B:281 , THR B:293BINDING SITE FOR RESIDUE EDO B 19
19CC1SOFTWAREGLY A:226 , LYS A:229 , HOH A:390BINDING SITE FOR RESIDUE EDO A 20
20CC2SOFTWAREHOH A:30 , HOH A:195 , LYS A:225 , VAL A:287 , GLY A:290 , LEU A:291 , HIS C:267 , HOH C:368BINDING SITE FOR RESIDUE EDO C 21
21CC3SOFTWAREEDO A:23 , EDO A:24 , HIS A:224 , HOH A:409 , HOH C:344 , HOH C:423BINDING SITE FOR RESIDUE EDO A 22
22CC4SOFTWAREEDO A:22 , EDO A:24 , EDO C:11 , HIS C:224 , HOH C:423BINDING SITE FOR RESIDUE EDO A 23
23CC5SOFTWAREEDO A:7 , EDO A:22 , EDO A:23 , TRP A:231 , LYS A:279 , HOH A:409BINDING SITE FOR RESIDUE EDO A 24
24CC6SOFTWARETYR B:303 , LYS B:305 , ASN B:306 , LYS B:307 , ASP B:341 , HOH B:391BINDING SITE FOR RESIDUE EDO B 25
25CC7SOFTWAREEDO B:19 , HIS B:224 , SER B:266 , HIS B:267 , GLU B:268 , LYS B:279 , LEU B:280 , THR B:281 , HOH B:345BINDING SITE FOR RESIDUE EDO B 26
26CC8SOFTWAREEDO B:3 , EDO B:32 , TRP B:231 , LYS B:279 , HOH B:345BINDING SITE FOR RESIDUE EDO B 27
27CC9SOFTWAREEDO B:10 , GLY B:226 , LYS B:229BINDING SITE FOR RESIDUE EDO B 28
28DC1SOFTWAREHOH B:14 , LYS B:225 , HIS B:267 , VAL B:287 , LEU B:291 , HOH B:346 , HOH B:395BINDING SITE FOR RESIDUE EDO B 30
29DC2SOFTWARESER B:272 , PHE B:273BINDING SITE FOR RESIDUE EDO B 31
30DC3SOFTWAREEDO B:27 , HIS B:224 , HOH B:345BINDING SITE FOR RESIDUE EDO B 32
31DC4SOFTWAREVAL B:319BINDING SITE FOR RESIDUE EDO B 33
32DC5SOFTWAREASP C:260 , GLY C:261 , LYS C:263 , PRO C:284BINDING SITE FOR RESIDUE EDO C 34
33DC6SOFTWARETYR C:303 , LYS C:305 , ASN C:306 , ASP C:341BINDING SITE FOR RESIDUE EDO C 35
34DC7SOFTWAREHOH B:130 , GLY B:256 , TYR B:257 , GLY B:258 , PRO B:284 , THR B:286 , ASP B:289BINDING SITE FOR RESIDUE EDO B 37
35DC8SOFTWAREGLY C:226 , LYS C:229BINDING SITE FOR RESIDUE EDO C 38
36DC9SOFTWARESER B:206 , TRP B:207BINDING SITE FOR RESIDUE EDO B 39
37EC1SOFTWARETYR A:303 , LYS A:305 , ASN A:306 , LYS A:307 , ASP A:341 , HOH A:385BINDING SITE FOR RESIDUE EDO A 40
38EC2SOFTWARESER A:206 , TRP A:207BINDING SITE FOR RESIDUE EDO A 41

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QVE)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AXHPS51148 AXH domain profile.HBP1_HUMAN203-345
 
 		  3A:207-342
B:207-342
C:207-342
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AXHPS51148 AXH domain profile.HBP1_HUMAN203-345
 
 		  1A:207-342
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AXHPS51148 AXH domain profile.HBP1_HUMAN203-345
 
 		  1-
B:207-342
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AXHPS51148 AXH domain profile.HBP1_HUMAN203-345
 
 		  1-
-
C:207-342

(-) Exons   (4, 12)

Asymmetric Unit (4, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1dENST000002225741dENSE00001374924chr7:106809460-106809630171HBP1_HUMAN-00--
1.5eENST000002225745eENSE00000881751chr7:106820324-106820507184HBP1_HUMAN1-57570--
1.6eENST000002225746eENSE00000715119chr7:106822818-106823046229HBP1_HUMAN57-133770--
1.7ENST000002225747ENSE00000715126chr7:106826246-106826387142HBP1_HUMAN133-180480--
1.8aENST000002225748aENSE00000715132chr7:106826806-106826917112HBP1_HUMAN181-218383A:-1-218 (gaps)
B:-1-218 (gaps)
C:0-218 (gaps)		25
25
27
1.9ENST000002225749ENSE00000715138chr7:106827014-106827126113HBP1_HUMAN218-255383A:218-255 (gaps)
B:218-255 (gaps)
C:218-255 (gaps)		38
38
38
1.10ENST0000022257410ENSE00000715143chr7:106829737-106829893157HBP1_HUMAN256-308533A:256-308
B:256-308
C:256-308		53
53
53
1.11bENST0000022257411bENSE00000715147chr7:106830618-106830762145HBP1_HUMAN308-356493A:308-342
B:308-342
C:308-342		35
35
35
1.12bENST0000022257412bENSE00000715151chr7:106836279-106836596318HBP1_HUMAN356-4621070--
1.13bENST0000022257413bENSE00001432769chr7:106840605-106840746142HBP1_HUMAN462-509480--
1.14eENST0000022257414eENSE00001829379chr7:106841859-1068429741116HBP1_HUMAN510-51450--

(-) 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:130
 aligned with HBP1_HUMAN | O60381 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:149
                                   203       213       223       233       243       253       263       273       283       293       303       313       323       333         
           HBP1_HUMAN   194 SLSDDDDLGWCNSWPSTVWHCFLKGTRLCFHKGSNKEWQDVEDFARAEGCDNEEDLQMGIHKGYGSDGLKLLSHEESVSFGESVLKLTFDPGTVEDGLLTVECKLDHPFYVKNKGWSSFYPSLTVVQHGIPCCEVHIGDVCLPPGHPDA 342
               SCOP domains d3q          vea_ A: automated matches                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...----------.............eeee........eehhhhhhhh.---------..........eeeeeeeeeee..eeeeeeeee..hhhhh.eeeeee...eeee...eeee.hhhhhhhhhh...ee.....ee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------AXH  PDB: A:207-342 UniProt: 203-345                                                                                                         PROSITE
           Transcript 1 (1) Exon 1.8a [INCOMPLETE]   -------------------------------------Exon 1.10  PDB: A:256-308 UniProt: 256-308           ---------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.9  PDB: A:218-255 (gaps)       ----------------------------------------------------Exon 1.11b  PDB: A:308-342          Transcript 1 (2)
                 3qve A  -1 SMS----------WPSTVWHCFLKGTRLCFHKGSNKEWQDVEDFARAEG---------GIHKGYGSDGLKLLSHEESVSFGESVLKLTFDPGTVEDGLLTVECKLDHPFYVKNKGWSSFYPSLTVVQHGIPCCEVHIGDVCLPPGHPDA 342
                             ||      -   |   213       223       233        |-       253       263       273       283       293       303       313       323       333         
                             0|        207                                242       252                                                                                          
                            206                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:130
 aligned with HBP1_HUMAN | O60381 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:149
                                   203       213       223       233       243       253       263       273       283       293       303       313       323       333         
           HBP1_HUMAN   194 SLSDDDDLGWCNSWPSTVWHCFLKGTRLCFHKGSNKEWQDVEDFARAEGCDNEEDLQMGIHKGYGSDGLKLLSHEESVSFGESVLKLTFDPGTVEDGLLTVECKLDHPFYVKNKGWSSFYPSLTVVQHGIPCCEVHIGDVCLPPGHPDA 342
               SCOP domains d3q          veb_ B: automated matches                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...----------.............eeee........eehhhhhhhh.---------..........eeeeeeeeeee..eeeeeeeee..hhhhh.eeeee.....eee...eeee.hhhhhhhhhh...ee.....ee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------AXH  PDB: B:207-342 UniProt: 203-345                                                                                                         PROSITE
           Transcript 1 (1) Exon 1.8a [INCOMPLETE]   -------------------------------------Exon 1.10  PDB: B:256-308 UniProt: 256-308           ---------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.9  PDB: B:218-255 (gaps)       ----------------------------------------------------Exon 1.11b  PDB: B:308-342          Transcript 1 (2)
                 3qve B  -1 SMS----------WPSTVWHCFLKGTRLCFHKGSNKEWQDVEDFARAEG---------GIHKGYGSDGLKLLSHEESVSFGESVLKLTFDPGTVEDGLLTVECKLDHPFYVKNKGWSSFYPSLTVVQHGIPCCEVHIGDVCLPPGHPDA 342
                             ||      -   |   213       223       233        |-       253       263       273       283       293       303       313       323       333         
                             0|        207                                242       252                                                                                          
                            206                                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:129
 aligned with HBP1_HUMAN | O60381 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:151
                                   201       211       221       231       241       251       261       271       281       291       301       311       321       331       341 
           HBP1_HUMAN   192 MSSLSDDDDLGWCNSWPSTVWHCFLKGTRLCFHKGSNKEWQDVEDFARAEGCDNEEDLQMGIHKGYGSDGLKLLSHEESVSFGESVLKLTFDPGTVEDGLLTVECKLDHPFYVKNKGWSSFYPSLTVVQHGIPCCEVHIGDVCLPPGHPDA 342
               SCOP domains d3             qvec_ C: automated matches                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --             --------AXH-3qveC01 C:215-340                                                                                                         -- Pfam domains (1)
           Pfam domains (2) --             --------AXH-3qveC02 C:215-340                                                                                                         -- Pfam domains (2)
           Pfam domains (3) --             --------AXH-3qveC03 C:215-340                                                                                                         -- Pfam domains (3)
         Sec.struct. author ..-------------.............eeee........eehhhhhhhh.---------..........eeeeeeeeeee..eeeeeeeee........eeeee.....eee...eeee.hhhhhhhhhh...ee.....ee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------AXH  PDB: C:207-342 UniProt: 203-345                                                                                                         PROSITE
           Transcript 1 (1) Exon 1.8a UniProt: 181-218 -------------------------------------Exon 1.10  PDB: C:256-308 UniProt: 256-308           ---------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.9  PDB: C:218-255 (gaps)       ----------------------------------------------------Exon 1.11b  PDB: C:308-342          Transcript 1 (2)
                 3qve C   0 MS-------------WPSTVWHCFLKGTRLCFHKGSNKEWQDVEDFARAEG---------GIHKGYGSDGLKLLSHEESVSFGESVLKLTFDPGTVEDGLLTVECKLDHPFYVKNKGWSSFYPSLTVVQHGIPCCEVHIGDVCLPPGHPDA 342
                            ||       -     | 211       221       231       241|        -|      261       271       281       291       301       311       321       331       341 
                            0|           207                                242       252                                                                                          
                           206
   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, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QVE)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: AXH] (2)
(-)
Family: AXH (2)
(-)
Homo sapiens (Human) (1)
1aAXH-3qveC01C:215-340
1bAXH-3qveC02C:215-340
1cAXH-3qveC03C:215-340

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (HBP1_HUMAN | O60381)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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).
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:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0043268    positive regulation of potassium ion transport    Any process that activates or increases the frequency, rate or extent of the directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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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