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(-) Description

Title :  A THREE DIMENSIONAL MOVIE OF STRUCTURAL CHANGES IN BACTERIORHODOPSIN: STRUCTURE OBTAINED 13.8 US AFTER PHOTOEXCITATION
 
Authors :  A. Royant, E. Nango, T. Nakane, T. Tanaka, T. Arima, R. Neutze, S. Iwata
Date :  15 Oct 16  (Deposition) - 21 Dec 16  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Bacteriorhodopsin, Xfel, Time-Resolved Serial Femtosecond Crystallography, Sacla, Proton Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Nango, A. Royant, M. Kubo, T. Nakane, C. Wickstrand, T. Kimura, T. Tanaka, K. Tono, C. Song, R. Tanaka, T. Arima, A. Yamashita, J. Kobayashi, T. Hosaka, E. Mizohata, P. Nogly, M. Sugahara, D. Nam, T. Nomura, T. Shimamura, D. Im, T. Fujiwara, Y. Yamanaka, B. Jeon, T. Nishizawa, K. Oda, M. Fukuda, R. Andersson, P. Bath, R. Dods, J. Davidsson, S. Matsuoka, S. Kawatake, M. Murata, O. Nureki, S. Owada T. Kameshima, T. Hatsui, Y. Joti, G. Schertler, M. Yabashi, A. N. Bondar, J. Standfuss, R. Neutze, S. Iwata
A Three-Dimensional Movie Of Structural Changes In Bacteriorhodopsin
Science V. 354 1552 2016
PubMed-ID: 28008064  |  Reference-DOI: 10.1126/SCIENCE.AAH3497

(-) Compounds

Molecule 1 - BACTERIORHODOPSIN
    ChainsA
    FragmentUNP RESIDUES 14-261
    Organism CommonHALOBACTERIUM SP. NRC-1
    Organism ScientificHALOBACTERIUM SALINARUM NRC-1
    Organism Taxid64091
    StrainNRC-1
    SynonymBR,BACTERIOOPSIN,BO

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 16)

Asymmetric Unit (10, 16)
No.NameCountTypeFull Name
1C141Ligand/IonTETRADECANE
2D101Ligand/IonDECANE
3DD91Ligand/IonNONANE
4HP61Ligand/IonHEPTANE
5L2P3Ligand/Ion2,3-DI-PHYTANYL-GLYCEROL
6MYS2Ligand/IonPENTADECANE
7OCT3Ligand/IonN-OCTANE
8RET1Ligand/IonRETINAL
9TRD1Ligand/IonTRIDECANE
10UND2Ligand/IonUNDECANE
Biological Unit 1 (10, 48)
No.NameCountTypeFull Name
1C143Ligand/IonTETRADECANE
2D103Ligand/IonDECANE
3DD93Ligand/IonNONANE
4HP63Ligand/IonHEPTANE
5L2P9Ligand/Ion2,3-DI-PHYTANYL-GLYCEROL
6MYS6Ligand/IonPENTADECANE
7OCT9Ligand/IonN-OCTANE
8RET3Ligand/IonRETINAL
9TRD3Ligand/IonTRIDECANE
10UND6Ligand/IonUNDECANE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:86 , THR A:90 , MET A:118 , TRP A:138 , SER A:141 , TRP A:182 , TYR A:185 , PRO A:186 , ASP A:212 , ALA A:215 , LYS A:216binding site for residue RET A 300
02AC2SOFTWAREALA A:44 , LEU A:48 , PHE A:54 , THR A:107 , TYR A:147 , D10 A:602binding site for residue L2P A 600
03AC3SOFTWARELEU A:149 , SER A:183binding site for residue TRD A 601
04AC4SOFTWARELEU A:22 , L2P A:600 , HP6 A:603binding site for residue D10 A 602
05AC5SOFTWARED10 A:602binding site for residue HP6 A 603
06AC6SOFTWARELYS A:172binding site for residue OCT A 604
07AC7SOFTWAREMYS A:606binding site for residue OCT A 605
08AC8SOFTWAREOCT A:605 , L2P A:608binding site for residue MYS A 606
09AC9SOFTWAREL2P A:608binding site for residue UND A 607
10AD1SOFTWARETYR A:131 , TRP A:138 , ILE A:203 , MYS A:606 , UND A:607binding site for residue L2P A 608
11AD2SOFTWAREILE A:52 , MET A:56 , TYR A:64 , TRP A:80 , ALA A:84 , GLY A:116 , ILE A:117 , GLY A:120 , LEU A:123 , VAL A:124 , C14 A:612binding site for residue L2P A 609
12AD3SOFTWARETYR A:26binding site for residue MYS A 610
13AD4SOFTWAREARG A:225binding site for residue DD9 A 611
14AD5SOFTWARELEU A:87 , PRO A:91 , LEU A:95 , L2P A:609binding site for residue C14 A 612
15AD6SOFTWARETYR A:26binding site for residue OCT A 613

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H2M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5H2M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H2M)

(-) Exons   (0, 0)

(no "Exon" information available for 5H2M)

(-) 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:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h2m A   4 ITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAE 234
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233 

   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 5H2M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H2M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H2M)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BACR_HALSA | P029451ap9 1at9 1bac 1bad 1bct 1bha 1bhb 1bm1 1brd 1brr 1brx 1c3w 1c8r 1c8s 1cwq 1dze 1e0p 1f4z 1f50 1fbb 1fbk 1iw6 1iw9 1ixf 1jv6 1jv7 1kg8 1kg9 1kgb 1kme 1l0m 1m0k 1m0l 1m0m 1mgy 1o0a 1p8h 1p8i 1p8u 1pxr 1pxs 1py6 1q5i 1q5j 1qhj 1qko 1qkp 1qm8 1r2n 1r84 1s51 1s52 1s53 1s54 1s8j 1s8l 1tn0 1tn5 1ucq 1vjm 1x0i 1x0k 1x0s 1xji 2at9 2brd 2i1x 2i20 2i21 2ntu 2ntw 2wjk 2wjl 2zfe 2zzl 3coc 3cod 3han 3hao 3hap 3haq 3har 3has 3mbv 3ns0 3nsb 3t45 3utv 3utw 3utx 3uty 3vhz 3vi0 4fpd 4hwl 4hyx 4md1 4md2 4ov0 4x31 4x32 4xxj 5a44 5a45 5b34 5b35 5b6v 5b6w 5b6x 5b6y 5b6z 5br2 5br5 5h2h 5h2i 5h2j 5h2k 5h2l 5h2n 5h2o 5h2p 5j7a 5vn7 5vn9

(-) Related Entries Specified in the PDB File

5b6v 5b6w 5b6x 5b6y 5b6z 5h2h 5h2i 5h2j 5h2k 5h2l 5h2n 5h2o 5h2p