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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOTOSYNTHETIC REACTION CENTER FROM A THERMOPHILIC BACTERIUM, THERMOCHROMATIUM TEPIDUM
 
Authors :  T. Nogi, I. Fathir, M. Kobayashi, T. Nozawa, K. Miki
Date :  08 May 00  (Deposition) - 13 Dec 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  C,H,L,M
Keywords :  Membrane Protein Complex, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nogi, I. Fathir, M. Kobayashi, T. Nozawa, K. Miki
Crystal Structures Of Photosynthetic Reaction Center And High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum: Thermostability And Electron Transfer.
Proc. Natl. Acad. Sci. Usa V. 97 13561 2000
PubMed-ID: 11095707  |  Reference-DOI: 10.1073/PNAS.240224997
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOTOSYNTHETIC REACTION CENTER
    Chains: C
    Fragment: CYTOCHROME SUBUNIT
    Organism Scientific: THERMOCHROMATIUM TEPIDUM
    Organism Taxid: 1050
 
Molecule 2 - PHOTOSYNTHETIC REACTION CENTER
    Chains: L
    Fragment: L SUBUNIT
    Organism Scientific: THERMOCHROMATIUM TEPIDUM
    Organism Taxid: 1050
 
Molecule 3 - PHOTOSYNTHETIC REACTION CENTER
    Chains: M
    Fragment: M SUBUNIT
    Organism Scientific: THERMOCHROMATIUM TEPIDUM
    Organism Taxid: 1050
 
Molecule 4 - PHOTOSYNTHETIC REACTION CENTER
    Chains: H
    Fragment: H SUBUNIT
    Organism Scientific: THERMOCHROMATIUM TEPIDUM
    Organism Taxid: 1050

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : CHLM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 21)

Asymmetric/Biological Unit (9, 21)
No.NameCountTypeFull Name
1BCL4Ligand/IonBACTERIOCHLOROPHYLL A
2BGL6Ligand/IonB-2-OCTYLGLUCOSIDE
3BPH2Ligand/IonBACTERIOPHEOPHYTIN A
4CRT1Ligand/IonSPIRILLOXANTHIN
5FE1Ligand/IonFE (III) ION
6HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
7LDA1Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
8MQ81Ligand/IonMENAQUINONE 8
9PEF1Ligand/IonDI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU L:183 , SER L:186BINDING SITE FOR RESIDUE BGL L 701
02AC2SOFTWARETYR C:152 , PHE M:72 , ASN M:73 , ALA M:76 , TRP M:80 , TRP M:113BINDING SITE FOR RESIDUE BGL M 702
03AC3SOFTWAREASN L:68 , LEU L:69 , TRP L:70 , BGL L:704BINDING SITE FOR RESIDUE BGL L 703
04AC4SOFTWAREGLN H:13 , ILE H:16 , TRP H:20 , TRP L:70 , BCL L:604 , BGL L:703 , MET M:302BINDING SITE FOR RESIDUE BGL L 704
05AC5SOFTWARETRP M:129BINDING SITE FOR RESIDUE BGL M 705
06AC6SOFTWAREPHE H:22 , TYR H:29 , TRP M:270 , HOH M:930BINDING SITE FOR RESIDUE BGL M 706
07AC7SOFTWAREHIS L:198 , HIS L:238 , HIS M:218 , GLU M:233 , HIS M:265BINDING SITE FOR RESIDUE FE M 607
08AC8SOFTWAREHIS L:176 , MET L:182 , ILE L:185 , SER L:186 , PHE L:189 , THR L:190 , VAL L:228 , BCL L:602 , HOH L:914 , TRP M:128 , ILE M:178 , HIS M:181 , LEU M:182 , BCL M:603 , BPH M:605 , CRT M:613BINDING SITE FOR RESIDUE BCL M 601
09AC9SOFTWAREPHE L:105 , ALA L:132 , ALA L:135 , TYR L:136 , LEU L:139 , VAL L:165 , TYR L:170 , PHE L:175 , HIS L:176 , HIS L:181 , ALA L:184 , ILE L:185 , PHE L:188 , SER L:252 , CYS L:255 , ILE L:256 , BCL L:604 , TYR M:209 , BCL M:601 , BCL M:603BINDING SITE FOR RESIDUE BCL L 602
10BC1SOFTWAREPHE L:189 , BCL L:602 , BCL L:604 , ILE M:70 , ALA M:152 , PHE M:155 , THR M:185 , SER M:189 , LEU M:195 , TYR M:196 , HIS M:201 , SER M:204 , ILE M:205 , TYR M:209 , ALA M:279 , ILE M:283 , BCL M:601 , BPH M:605 , CRT M:613BINDING SITE FOR RESIDUE BCL M 603
11BC2SOFTWARETYR L:136 , PHE L:154 , ILE L:158 , HIS L:161 , LEU L:162 , BCL L:602 , BPH L:606 , BGL L:704 , MET M:202 , ILE M:205 , ALA M:206 , TYR M:209 , BCL M:603 , HOH M:897BINDING SITE FOR RESIDUE BCL L 604
12BC3SOFTWAREPHE L:189 , CYS L:192 , LEU L:193 , SER L:196 , ILE L:227 , VAL L:228 , LEU M:64 , ILE M:125 , TRP M:128 , PHE M:149 , VAL M:276 , BCL M:601 , BCL M:603BINDING SITE FOR RESIDUE BPH M 605
13BC4SOFTWAREILE L:49 , PHE L:105 , TRP L:108 , GLU L:112 , VAL L:125 , PHE L:129 , PHE L:131 , TYR L:156 , ALA L:249 , BCL L:604 , TYR M:209 , ALA M:212 , LEU M:213 , MET M:217 , MET M:255 , MQ8 M:608BINDING SITE FOR RESIDUE BPH L 606
14BC5SOFTWAREPEF H:708 , PHE L:29 , GLY L:35 , PHE L:39 , TRP L:108 , BPH L:606 , LEU M:213 , MET M:217 , HIS M:218 , THR M:221 , TRP M:251 , ASN M:258 , ALA M:259 , THR M:260 , TRP M:267BINDING SITE FOR RESIDUE MQ8 M 608
15BC6SOFTWARETYR C:54 , GLN C:55 , SER C:56 , VAL C:57 , GLN C:58 , VAL C:59 , LEU C:60 , PHE C:68 , MET C:72 , VAL C:75 , THR C:76 , CYS C:85 , CYS C:88 , HIS C:89 , ALA C:95 , LYS C:102 , SER C:105 , ARG C:106 , VAL C:168 , ALA C:171 , SER C:172BINDING SITE FOR RESIDUE HEM C 609
16BC7SOFTWAREVAL C:75 , TYR C:87 , TYR C:100 , THR C:101 , VAL C:104 , SER C:105 , MET C:108 , CYS C:130 , CYS C:133 , HIS C:134 , PRO C:138 , VAL C:139 , LEU C:269 , ARG C:273 , LEU C:281 , VAL C:283BINDING SITE FOR RESIDUE HEM C 610
17BC8SOFTWAREILE C:188 , ARG C:189 , ILE C:190 , THR C:191 , PHE C:211 , MET C:214 , SER C:218 , GLY C:224 , CYS C:225 , CYS C:228 , HIS C:229 , PHE C:234 , ASN C:235 , ARG C:244 , ALA C:247 , TRP C:248 , ARG C:252 , HOH C:877 , HOH C:879 , ILE M:190 , TYR M:316BINDING SITE FOR RESIDUE HEM C 611
18BC9SOFTWAREHIS C:122 , VAL C:123 , THR C:126 , GLY C:127 , VAL C:128 , ILE C:217 , LYS C:243 , THR C:246 , ALA C:250 , VAL C:254 , VAL C:283 , SER C:284 , CYS C:285 , CYS C:288 , HIS C:289 , ASN C:293 , LYS C:294 , PRO C:295BINDING SITE FOR RESIDUE HEM C 612
19CC1SOFTWAREILE M:67 , GLY M:71 , PHE M:72 , PHE M:89 , ILE M:105 , TRP M:114 , LEU M:115 , GLY M:118 , LEU M:119 , THR M:122 , TYR M:156 , PHE M:161 , VAL M:174 , GLY M:177 , HIS M:181 , BCL M:601 , BCL M:603BINDING SITE FOR RESIDUE CRT M 613
20CC2SOFTWAREARG L:84 , MET L:85 , GLN L:95 , THR L:98 , VAL L:140 , TRP L:150BINDING SITE FOR RESIDUE LDA L 707
21CC3SOFTWAREARG H:31 , LYS H:35 , TYR H:39 , PHE L:29 , PHE M:207 , ARG M:252 , MET M:255 , GLY M:256 , PHE M:257 , MQ8 M:608BINDING SITE FOR RESIDUE PEF H 708

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EYS)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro C:4 -Pro C:5
2Tyr H:39 -Pro H:40
3Ala H:78 -Pro H:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EYS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EYS)

(-) Exons   (0, 0)

(no "Exon" information available for 1EYS)

(-) Sequences/Alignments

Asymmetric/Biological 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 C from PDB  Type:PROTEIN  Length:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d1eysc_ C: Photosynthetic reaction centre (cytochrome subunit)                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ----------------------1eysC01 C:23-140,C:294-310 Photosynthetic Reaction Center, subunit C, domain 2                                        1eysC02 C:141-192,C:202-293                         ---------1eysC02 C:141-192,C:202-293 Photosynthetic Reaction Center, subunit C, domain 2             1eysC01           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee........eeeehhhhhhhhhhhh..............hhhhhh.........hhhhhhhhhhhhhhhhh...hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh.............................hhhhhhhhh....hhhhhh...................hhhhhhhhhhhhhhhhhhhh.hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhh..........hhhhhhh...hhhhhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eys C   1 CEGPPPGTEQIGYRGVGMENYYVKRQRALSIQANQPVESLPAADSTGPKASEVYQSVQVLKDLSVGEFTRTMVAVTTWVSPKEGCNYCHVPGNWASDDIYTKVVSRRMFELVRAANSDWKAHVAETGVTCYTCHRGNPVPKYAWVTDPGPKYPSGLKPTGQNYGSKTVAYASLPFDPLTPFLDQANEIRITGNAALAGSNPASLKQAEWTFGLMMNISDSLGVGCTSCHNTRAFNDWTQSTPKRTTAWYAIRHVRDINQNYIWPLNDVLPASRKGPYGDPLRVSCMTCHQAVNKPLYGAQMAKDYPGLYK 310
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310


Chain H from PDB  Type:PROTEIN  Length:238
 aligned with Q93RD8_THETI | Q93RD8 from UniProtKB/TrEMBL  Length:255

    Alignment length:253
                                    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   
         Q93RD8_THETI     3 HYIDAAQITIWAFWLFFFGLIIYLRREDKREGYPLDSNRTERSGGRVKVVGFPDLPDPKTFVLPHNGGTVVAPRVEAPVAVNATPFSPAPGSPLVPNGDPMLSGFGPAACPDRPKHCDLTFEGLPKIVPMRVAKEFSIAEGDPDPRGMTVVGLDGEVAGTVSDVWVDRSEPQIRYLEVEVAANKKKVLLPIGFSRFDKKARKVKVDAIKAAHFANVPTLSNPDQVTLYEEDKVCAYYAGGKLYATAERAGPLL 255
               SCOP domains d1eysh2 H:7-43                       ---------------d1eysh1 H:59-259 Photosynthetic reaction centre                                                                                                                                                           SCOP domains
               CATH domains 1eysH01 H:7-118 Photosynthetic Reacti               on Center, subunit H, domain 1                              1eysH02 H:119-258 Photosynthetic Reaction Center, subunit H, domain 2                                                                       - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh.........---------------......eee........eee..........eee........eee........hhhhh..................ee.......ee..........eee.....eeeeeeeeeee....eeeeeeeee.....eeeee.hhheeehhh.eee....hhhhhhhh.........hhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eys H   7 HYIDAAQITIWAFWLFFFGLIIYLRREDKREGYPLDS---------------PDLPDPKTFVLPHNGGTVVAPRVEAPVAVNATPFSPAPGSPLVPNGDPMLSGFGPAASPDRPKHCDLTFEGLPKIVPMRVAKEFSIAEGDPDPRGMTVVGLDGEVAGTVSDVWVDRSEPQIRYLEVEVAANKKKVLLPIGFSRFDKKARKVKVDAIKAAHFANVPTLSNPDQVTLYEEDKVCAYYAGGKLYATAERAGPLL 259
                                    16        26        36      |  -         -  |     66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256   
                                                               43              59                                                                                                                                                                                                        


Chain L from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains d1eysl_ L: L (light) subunit                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1eysL01 L:1-171 Membrane spanning alpha-helix pairs                                                                                                                        1eysL02 L:172-271 Membrane spanning alpha-helix pairs                                               --------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.......hhhhh..ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eys L   1 AMLSFEKKYRVRGGTLIGGDLFDFWVGPFYVGFFGVVGFCFTLLGVLLIVWGATIGPTGPTSDLQTYNLWRISIAPPDLSYGLRMAPLTEGGLWQIITICAAGAFISWALREVEICRKLGIGFHVPFAFSFAIGAYLVLVFVRPLLMGAWGHGFPYGILSHLDWVSNVGYQFLHFHYNPAHMLAISFFFTNCLALSMHGSLILSVTNPQRGEPVKTSEHENTFFRDIVGYSIGALAIHRLGLFLALSAAFWSAVCILISGPFWTRGWPEWWNWWLELPLW 280
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280


Chain M from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d1eysm_ M: M (medium) subunit                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1eysM01 M:1-142 Membrane spanning alpha-helix pairs                                                                                           1eysM02 M:143-301 Membrane spanning alpha-helix pairs                                                                                                          ----------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........ee........................hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1eys M   1 PEYQNIFTAVQVRAPAYPGVPLPKGNLPRIGRPIFSYWLGKIGDAQIGPIYLGLTGTLSIFFGLVAISIIGFNMLASVHWDVFQFLKHFFWLGLEPPPPQYGLRIPPLSEGGWWLIAGLFLTLSILLWWVRTYKRAEALGMSQHLSWAFAAAIFFYLVLGFIRPVMMGSWAKAVPFGIFPHLDWTAAFSIRYGNLYYNPFHMLSIAFLYGSALLFAMHGATILSVSRFGGDREIDQITHRGTAAEGAALFWRWTMGFNATMESIHRWAWWCAVLTVITAGIGILLSGTVVDNWYLWAVKHGMAPAYPEVVTAVNPYET 318
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
   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  (5, 5)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (4, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EYS)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (Q93RD8_THETI | Q93RD8)
molecular function
    GO:0045156    electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity    Enables the directed movement of electrons within the cyclic electron transport pathway of photosynthesis.
biological process
    GO:0019684    photosynthesis, light reaction    The light reactions of photosynthesis, which take place in photosystems II and I. Light energy is harvested and used to power the transfer of electrons among a series of electron donors and acceptors. The final electron acceptor is NADP+, which is reduced to NADPH. NADPH generated from light reactions is used in sugar synthesis in dark reactions. Light reactions also generate a proton motive force across the thylakoid membrane, and the proton gradient is used to synthesize ATP. There are two chemical reactions involved in the light reactions: water oxidation in photosystem II, and NADP reduction in photosystem I.
cellular component
    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:0030077    plasma membrane light-harvesting complex    A plasma membrane protein-pigment complex that may be closely or peripherally associated to photosynthetic reaction centers that participate in harvesting and transferring radiant energy to the reaction center. Examples of this complex are found in bacterial species.

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