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(-) Description

Title :  REFINED STRUCTURE OF GLYCOPHORIN A TRANSMEMBRANE SEGMENT DIMER IN DPC MICELLES
 
Authors :  K. S. Mineev, E. V. Bocharov, M. V. Goncharuk, A. S. Arseniev, P. E. Volyn R. G. Efremov
Date :  13 Oct 09  (Deposition) - 22 Sep 10  (Release) - 25 Jul 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Glycophorin A, Transmembrane Dimer, Micelles, Blood Group Antigen, Cell Membrane, Glycoprotein, Host-Virus Interaction, Membrane, Sialic Acid, Transmembrane, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. S. Mineev, E. V. Bocharov, P. E. Volynsky, M. V. Goncharuk, E. N. Tkach, Y. S. Ermolyuk, A. A. Schulga, V. V. Chupin, I. V. Maslennikov, R. G. Efremov, A. S. Arseniev
Dimeric Structure Of The Transmembrane Domain Of Glycophori A In Lipidic And Detergent Environments.
Acta Naturae V. 3 90 2011
PubMed-ID: 22649687

(-) Compounds

Molecule 1 - GLYCOPHORIN-A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PGEMEX
    Fragment: TRANSMEMBRANE SEGMENT (UNP RESIDUES 89-117)
    Gene: GYPA, GPA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PAS-2, SIALOGLYCOPROTEIN ALPHA, MN SIALOGLYCOPROTEIN

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x): AB
NMR Structure * (1x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2KPE)

(-) Sites  (0, 0)

(no "Site" information available for 2KPE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOPHORIN_APS00312 Glycophorin A signature.GLPA_HUMAN95-104
 		  2A:76-85
B:76-85
NMR Structure * (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOPHORIN_APS00312 Glycophorin A signature.GLPA_HUMAN95-104
 		  2A:76-85
B:76-85

(-) Exons   (2, 4)

NMR Structure (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003607711aENSE00001721810chr4:145061904-145061752153GLPA_HUMAN1-13130--
1.3ENST000003607713ENSE00001680915chr4:145041741-14504164399GLPA_HUMAN13-46340--
1.4aENST000003607714aENSE00001139681chr4:145040934-14504083996GLPA_HUMAN46-78330--
1.5aENST000003607715aENSE00001139707chr4:145039905-14503986739GLPA_HUMAN78-91142A:70-72
B:70-72		3
3
1.6aENST000003607716aENSE00001139697chr4:145038092-14503800786GLPA_HUMAN91-119292A:72-98
B:72-98		27
27
1.7bENST000003607717bENSE00001133833chr4:145035920-14503584279GLPA_HUMAN120-146270--
1.8fENST000003607718fENSE00001200737chr4:145032563-1450304572107GLPA_HUMAN146-15050--

(-) Sequences/Alignments

NMR Structure
   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:29
 aligned with GLPA_HUMAN | P02724 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:29
                                    98       108         
           GLPA_HUMAN    89 EPEITLIIFGVMAGVIGTILLISYGIRRL 117
               SCOP domains ----------------------------- SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ------GLYCOPHORI------------- PROSITE
           Transcript 1 (1) 1.5-------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.6a  PDB: A:72-98     Transcript 1 (2)
                 2kpe A  70 EPEITLIIFGVMAGVIGTILLISYGIRRL  98
                                    79        89         


Chain B from PDB  Type:PROTEIN  Length:29
 aligned with GLPA_HUMAN | P02724 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:29
                                    98       108         
           GLPA_HUMAN    89 EPEITLIIFGVMAGVIGTILLISYGIRRL 117
               SCOP domains ----------------------------- SCOP domains
               CATH domains ----------------------------- CATH domains
           Pfam domains (1) Glycophorin_A-2kpeB01 B:70-98 Pfam domains (1)
           Pfam domains (2) Glycophorin_A-2kpeB02 B:70-98 Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ------GLYCOPHORI------------- PROSITE
           Transcript 1 (1) 1.5-------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.6a  PDB: B:72-98     Transcript 1 (2)
                 2kpe B  70 EPEITLIIFGVMAGVIGTILLISYGIRRL  98
                                    79        89
   Legend:   → Mismatch (orange background)
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  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 2KPE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: no clan defined [family: Glycophorin_A] (2)

(-) Gene Ontology  (8, 8)

NMR Structure(hide GO term definitions)
Chain A,B   (GLPA_HUMAN | P02724)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0001618    virus receptor activity    Combining with a virus component and mediating entry of the virus into the cell.
biological process
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  2kpe
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 Related Entries

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

UniProtKB/Swiss-Prot
        GLPA_HUMAN | P02724: 1afo 1msr 2kpf 5eh4 5eh6

(-) Related Entries Specified in the PDB File

7208 NMR ASSIGNMENT
2kpf