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(-) Description

Title :  CRYSTAL STRUCTURE OF TWO HMGB1 BOX A DOMAINS COOPERATING TO UNDERWIND AND KINK A DNA
 
Authors :  R. Sanchez-Giraldo, F. J. Acosta-Reyes, C. S. Malarkey, N. Saperas, M. E. A. Churchill, J. L. Campos
Date :  30 Jun 14  (Deposition) - 01 Jul 15  (Release) - 29 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Hmg-Box, Hmgb1, Box A Domain, High Mobility Group, Dna-Binding, Bend Dna, Kink Dna, Architectural Factor, Minor Groove, Chromatin, Nucleus, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Sanchez-Giraldo, F. J. Acosta-Reyes, C. S. Malarkey, N. Saperas, M. E. Churchill, J. L. Campos
Two High-Mobility Group Box Domains Act Together To Underwind And Kink Dna.
Acta Crystallogr. , Sect. D V. 71 1423 2015
PubMed-ID: 26143914  |  Reference-DOI: 10.1107/S1399004715007452

(-) Compounds

Molecule 1 - HIGH MOBILITY GROUP PROTEIN B1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX2T
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 8-81
    Gene: HMGB1, HMG-1, HMG1
    Organism Common: BROWN RAT,RAT,RATS
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: AMPHOTERIN, HEPARIN-BINDING PROTEIN P30, HIGH MOBILITY GROUP PROTEIN 1, HMG-1
 
Molecule 2 - DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3')
    Chains: C, D, E, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH C:107 , HOH C:113 , HOH C:116 , HOH D:205 , HOH D:226 , HOH D:227BINDING SITE FOR RESIDUE MG D 101

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:44

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4QR9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QR9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QR9)

(-) Exons   (0, 0)

(no "Exon" information available for 4QR9)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:75
                                                                                                          
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                  4qr9 A  5 GSKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIP 79
                                    14        24        34        44        54        64        74     


Chain B from PDB  Type:PROTEIN  Length:75
                                                                                                          
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                  4qr9 B  5 GSKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIP 79
                                    14        24        34        44        54        64        74     


Chain C from PDB  Type:DNA  Length:10
                                         
                  4qr9 C  1 ATATCGATAT 10
                                    10


Chain D from PDB  Type:DNA  Length:10
                                         
                  4qr9 D 11 ATATCGATAT 20
                                    20


Chain E from PDB  Type:DNA  Length:10
                                         
                  4qr9 E  1 ATATCGATAT 10
                                    10


Chain F from PDB  Type:DNA  Length:10
                                         
                  4qr9 F 11 ATATCGATAT 20
                                    20
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4QR9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QR9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QR9)

(-) Gene Ontology  (76, 76)

Asymmetric/Biological Unit(hide GO term definitions)

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  4qr9
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  HMGB1_RAT | P63159
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 Related Entries

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

UniProtKB/Swiss-Prot
        HMGB1_RAT | P63159: 1aab 1ckt 1hme 1hmf 2gzk

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