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(-) Description

Title :  STRUCTURE OF SPX DOMAIN OF THE YEAST INORGANIC POLYPHOPHATE POLYMERASE VTC4 CRYSTALLIZED BY CARRIER-DRIVEN CRYSTALLIZATION IN FUSION WITH THE MACRO DOMAIN OF HUMAN HISTONE MACROH2A1.1
 
Authors :  R. Wild, M. Hothorn
Date :  03 Aug 16  (Deposition) - 09 Nov 16  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.29
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Macro Domain, Spx Domain, Inositol Polyphosphate Binding, Carrier- Driven Crystallization, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Wild, M. Hothorn
The Macro Domain As Fusion Tag For Carrier-Driven Crystallization.
Protein Sci. V. 26 365 2017
PubMed-ID: 27774698  |  Reference-DOI: 10.1002/PRO.3073

(-) Compounds

Molecule 1 - VACUOLAR TRANSPORTER CHAPERONE 4,CORE HISTONE MACRO-H2A.1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMH-MACROHC
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: DE3 RIL
    Expression System Vector Type: PLASMID
    Gene: VTC4, PHM3, YJL012C, J1345, H2AFY, MACROH2A1
    Organ: VACUOLE
    Organism Common: BAKER'S YEAST, HUMAN
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C), HOMO SAPIENS
    Organism Taxid: 559292, 9606
    Synonym: PHOSPHATE METABOLISM PROTEIN 3,MH2A1,HISTONE H2A.Y,H2A/Y, MEDULLOBLASTOMA ANTIGEN MU-MB-50.205

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5LNC)

(-) Sites  (0, 0)

(no "Site" information available for 5LNC)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LNC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LNC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LNC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LNC)

(-) Exons   (0, 0)

(no "Exon" information available for 5LNC)

(-) Sequences/Alignments

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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:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh....eeee.....eeeee..hhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.......eeeeee.......hhhhhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lnc A   2 KFGEHLSKSLIRQYSYYYISYDDLKTELEDNLSKNNGTQELETDFLESLEIELDKVYTFCKVKHSEVFRRVKEVQEQVQHTVRLLDSNNPPTQLDFEILEEELSDIIADVHDLAKFSRLNYTGFQKIIKKHDKKTGFILKPVFQVRLDSKPFFKENYDELVVKISQLYDIARTSGAFTVLSTKSLFLGQKLQVVQADIASIDSDAVVHPTNTDFYIGGEVGNTLEKKGGKEFVEAVLELRKKNGPLEVAGAAVSAGHGLPAKFVIHCNSPVWGADKCEELLEKTVKNCLALADDKKLKSIAFPSIGSGRNGFPKQTAAQLILKAISSYFVSTMSSSIKTVYFVLFDSESIGIYVQEMAKLEHHH 371
                                    11        21        31      ||43        53        63        73        83        93       103       113       123       133       143       153       163       173     ||187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367    
                                                               38|                                                                                                                                       179|                                                                                                                                                                                           
                                                                41                                                                                                                                        184                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.......eeeeee.....eeeee..hhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.......eeeeee.......hhhhhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lnc B   3 FGEHLSKSLIRQYSYYYISYDDLKTELEDNLSKNNGQWTQELETDFLESLEIELDKVYTFCKVKHSEVFRRVKEVQEQVQHTVRLLDSNNPPTQLDFEILEEELSDIIADVHDLAKFSRLNYTGFQKIIKKHDKKTGFILKPVFQVRLDSKPFFKENYDELVVKISQLYDIARTSGAGSDGFTVLSTKSLFLGQKLQVVQADIASIDSDAVVHPTNTDFYIGGEVGNTLEKKGGKEFVEAVLELRKKNGPLEVAGAAVSAGHGLPAKFVIHCNSPVWGADKCEELLEKTVKNCLALADDKKLKSIAFPSIGSGRNGFPKQTAAQLILKAISSYFVSTMSSSIKTVYFVLFDSESIGIYVQEMAKLEH 369
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
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  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 5LNC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LNC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LNC)

(-) Gene Ontology  (63, 64)

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  VTC4_YEAST | P47075
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 Related Entries

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

UniProtKB/Swiss-Prot
        H2AY_HUMAN | O75367: 1u35 1zr3 1zr5 2f8n 2fxk 3hqh 3hsv 3iid 3iif 3ivb 5iit
        VTC4_YEAST | P47075: 3g3q 3g3r 3g3t 3g3u 5iig 5iiq 5iit

(-) Related Entries Specified in the PDB File

5iit 5IIT