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(-) Description

Title :  STRUCTURE OF THE REACTION CENTER FROM RHODOBACTER SPHAEROIDES R-26 AND 2.4.1: PROTEIN-COFACTOR (BACTERIOCHLOROPHYLL, BACTERIOPHEOPHYTIN, AND CAROTENOID) INTERACTIONS
 
Authors :  H. Komiya, T. O. Yeates, A. J. Chirino, D. C. Rees, J. P. Allen, G. Feher
Date :  09 Sep 91  (Deposition) - 31 Oct 93  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  H,L,M
Keywords :  Photosynthetic Reaction Center (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. O. Yeates, H. Komiya, A. Chirino, D. C. Rees, J. P. Allen, G. Feher
Structure Of The Reaction Center From Rhodobacter Sphaeroides R-26 And 2. 4. 1: Protein-Cofactor (Bacteriochlorophyll, Bacteriopheophytin, And Carotenoid) Interactions.
Proc. Natl. Acad. Sci. Usa V. 85 7993 1988
PubMed-ID: 3186702  |  Reference-DOI: 10.1073/PNAS.85.21.7993
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOTOSYNTHETIC REACTION CENTER
    ChainsL
    EngineeredYES
    Organism ScientificRHODOBACTER SPHAEROIDES
    Organism Taxid1063
 
Molecule 2 - PHOTOSYNTHETIC REACTION CENTER
    ChainsM
    EngineeredYES
    Organism ScientificRHODOBACTER SPHAEROIDES
    Organism Taxid1063
 
Molecule 3 - PHOTOSYNTHETIC REACTION CENTER
    ChainsH
    EngineeredYES
    Organism ScientificRHODOBACTER SPHAEROIDES
    Organism Taxid1063

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit HLM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1BCL4Ligand/IonBACTERIOCHLOROPHYLL A
2BOG1Ligand/IonB-OCTYLGLUCOSIDE
3BPH2Ligand/IonBACTERIOPHEOPHYTIN A
4FE1Ligand/IonFE (III) ION
5U102Ligand/IonUBIQUINONE-10

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREBCL L:282 , TRP M:66 , PHE M:67 , ILE M:70 , TYR M:177 , GLY M:178 , ILE M:179BINDING SITE FOR RESIDUE BOG M 308
02AC2SOFTWAREHIS L:190 , HIS L:230 , HIS M:219 , GLU M:234 , HIS M:266BINDING SITE FOR RESIDUE FE M 309
03AC3SOFTWAREHIS L:168 , MET L:174 , ILE L:177 , SER L:178 , THR L:182 , BCL L:283 , ILE M:179 , HIS M:182 , BOG M:308 , BCL M:310 , BPH M:312BINDING SITE FOR RESIDUE BCL L 282
04AC4SOFTWAREPHE L:97 , ALA L:124 , ALA L:127 , TYR L:128 , VAL L:157 , SER L:158 , GLY L:161 , TYR L:162 , PHE L:167 , HIS L:168 , HIS L:173 , ILE L:177 , PHE L:180 , SER L:244 , ALA L:245 , CYS L:247 , MET L:248 , BCL L:282 , BPH L:284 , TYR M:210 , BCL M:310 , BCL M:311BINDING SITE FOR RESIDUE BCL L 283
05AC5SOFTWAREPHE L:181 , BCL L:282 , BCL L:283 , ALA M:153 , ILE M:154 , LEU M:156 , TRP M:157 , LEU M:160 , THR M:186 , PHE M:197 , HIS M:202 , SER M:205 , ILE M:206 , LEU M:209 , TYR M:210 , VAL M:276 , GLY M:280 , ILE M:284 , BCL M:311 , BPH M:312BINDING SITE FOR RESIDUE BCL M 310
06AC6SOFTWAREPHE L:146 , LEU L:154 , VAL L:157 , BCL L:283 , BPH L:284 , PHE M:197 , GLY M:203 , ILE M:206 , ALA M:207 , BCL M:310BINDING SITE FOR RESIDUE BCL M 311
07AC7SOFTWAREPHE L:181 , ALA L:184 , LEU L:185 , ALA L:188 , LEU L:189 , LEU L:219 , BCL L:282 , SER M:59 , LEU M:60 , GLY M:63 , LEU M:64 , PHE M:67 , VAL M:126 , TRP M:129 , THR M:133 , THR M:146 , ALA M:149 , PHE M:150 , ALA M:153 , BCL M:310BINDING SITE FOR RESIDUE BPH M 312
08AC8SOFTWAREPHE L:41 , ALA L:42 , CYS L:92 , ALA L:93 , ALA L:96 , PHE L:97 , TRP L:100 , GLU L:104 , ILE L:117 , PHE L:121 , ALA L:124 , VAL L:241 , BCL L:283 , TYR M:210 , ALA M:213 , LEU M:214 , ALA M:217 , TRP M:252 , BCL M:311BINDING SITE FOR RESIDUE BPH L 284
09AC9SOFTWAREVAL L:31 , GLY L:35 , VAL L:36 , THR L:38 , ARG L:103 , MET M:218 , THR M:222 , ALA M:248 , ALA M:249 , TRP M:252 , MET M:256 , PHE M:258 , ASN M:259 , ALA M:260 , TRP M:268BINDING SITE FOR RESIDUE U10 M 313
10BC1SOFTWAREHIS L:190 , LEU L:193 , GLU L:212 , ASP L:213 , PHE L:216 , VAL L:220 , SER L:223 , ILE L:224 , GLY L:225 , THR L:226 , ILE L:229 , LEU L:232 , LEU M:60BINDING SITE FOR RESIDUE U10 L 285

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RCR)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly M:48 -Pro M:49
2Ala M:98 -Pro M:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RCR)

(-) 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 H from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains d4rcrh2 H:12-35         d4rcrh1 H:36-248 Photosynthetic reaction centre                                                                                                                                                                       SCOP domains
               CATH domains 4rcrH01 H:12-116 Photosynthetic Reaction Center, subunit H, domain 1                                     4rcrH02 H:117-248 Photosynthetic Reaction Center, subunit H, domain 2                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.hhhhhhh..........................eee......eee............................hhhhhh...........................................ee........eee.............eeeee.....eeeee....eee..eee.....................hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rcr H  12 LASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKR 248
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       

Chain L from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains d4rcrl_ L: L (light) subunit                                                                                                                                                                                                                                               SCOP domains
               CATH domains 4rcrL01 L:5-163 Membrane spanning alpha-helix pairs                                                                                                            4rcrL02 L:164-263 Membrane spanning alpha-helix pairs                                               ------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...............ee..ee...hhhhhhh.hhhhhhhhhhhhhhh..hhhhhh.....hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhh........hhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rcr L   5 FERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWNPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFAFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFFFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSAVFFSALCMIITGTIWFDQWVDWWQWWVKLP 270
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264      

Chain M from PDB  Type:PROTEIN  Length:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4rcrm_ M: M (medium) subunit                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 4rcrM01 M:6-143 Membrane spanning alpha-helix pairs                                                                                       4rcrM02 M:144-301 Membrane spanning alpha-helix pairs                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rcr M   6 IFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIADRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNH 301
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (4, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 74)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RCEH_RHOS4 | Q3J1701aig 1aij 1ds8 1dv3 1dv6 1e14 1e6d 1f6n 1fnp 1fnq 1jgw 1jgx 1jgy 1jgz 1jh0 1k6l 1k6n 1kby 1l9b 1l9j 1m3x 1mps 1ogv 1pcr 1pss 1pst 1qov 1rg5 1rgn 1rqk 1rvj 1ry5 1rzh 1rzz 1s00 1umx 1yf6 1yst 1z9j 1z9k 2bnp 2bns 2boz 2rcr 2wx5 4in5 4in6 4n7l 5lri
        RCEH_RHOSH | P0C0Y71aig 1aij 1ds8 1dv3 1dv6 1e14 1e6d 1f6n 1fnp 1fnq 1jgw 1jgx 1jgy 1jgz 1jh0 1k6l 1k6n 1kby 1l9b 1l9j 1m3x 1mps 1ogv 1pcr 1pss 1pst 1qov 1rg5 1rgn 1rqk 1rvj 1ry5 1rzh 1rzz 1s00 1umx 1yf6 1yst 1z9j 1z9k 2bnp 2bns 2boz 2gmr 2gnu 2hg3 2hg9 2hh1 2hhk 2hit 2hj6 2j8c 2j8d 2jiy 2jj0 2rcr 2uws 2uwt 2uwu 2uwv 2uww 2ux3 2ux4 2ux5 2uxj 2uxk 2uxl 2uxm 2wx5 3dsy 3dta 3dtr 3dts 3du2 3du3 3duq 3i4d 3v3y 3v3z 3zum 3zuw 4h99 4h9l 4hbh 4hbj 4in5 4in6 4in7 4lwy 4n7k 4n7l 4tqq 4v9g 5lse 5v33
        RCEL_RHOS4 | Q3J1A51aig 1aij 1ds8 1dv3 1dv6 1e14 1e6d 1f6n 1fnp 1fnq 1jgw 1jgx 1jgy 1jgz 1jh0 1k6l 1k6n 1kby 1l9b 1l9j 1m3x 1mps 1ogv 1pcr 1pss 1pst 1qov 1rg5 1rgn 1rqk 1rvj 1ry5 1rzh 1rzz 1s00 1umx 1yf6 1yst 1z9j 1z9k 2bnp 2bns 2boz 2gmr 2rcr 2wx5 4in5 4in6 4n7l 5lri
        RCEL_RHOSH | P0C0Y81aig 1aij 1ds8 1dv3 1dv6 1e14 1e6d 1f6n 1fnp 1fnq 1jgw 1jgx 1jgy 1jgz 1jh0 1k6l 1k6n 1kby 1l9b 1l9j 1m3x 1mps 1ogv 1pcr 1pss 1pst 1qov 1rg5 1rgn 1rqk 1rvj 1ry5 1rzh 1rzz 1s00 1umx 1yf6 1yst 1z9j 1z9k 2bnp 2bns 2boz 2gmr 2gnu 2hg3 2hg9 2hh1 2hhk 2hit 2hj6 2j8c 2j8d 2jiy 2jj0 2rcr 2uws 2uwt 2uwu 2uwv 2uww 2ux3 2ux4 2ux5 2uxj 2uxk 2uxl 2uxm 2wx5 3dsy 3dta 3dtr 3dts 3du2 3du3 3duq 3i4d 3v3y 3v3z 3zum 3zuw 4h99 4h9l 4hbh 4hbj 4in5 4in6 4in7 4lwy 4n7k 4n7l 4tqq 4v9g 5lse 5v33
        RCEM_RHOS4 | Q3J1A61aig 1aij 1ds8 1dv3 1dv6 1e14 1e6d 1f6n 1fnp 1fnq 1jgw 1jgx 1jgy 1jgz 1jh0 1k6l 1k6n 1kby 1l9b 1l9j 1m3x 1mps 1ogv 1pcr 1pss 1pst 1qov 1rg5 1rgn 1rqk 1rvj 1ry5 1rzh 1rzz 1s00 1umx 1yf6 1yst 1z9j 1z9k 2bnp 2bns 2boz 2rcr 2wx5 4in5 4in6 4n7l 5lri
        RCEM_RHOSH | P0C0Y91aig 1aij 1ds8 1dv3 1dv6 1e14 1e6d 1f6n 1fnp 1fnq 1jgw 1jgx 1jgy 1jgz 1jh0 1k6l 1k6n 1kby 1l9b 1l9j 1m3x 1mps 1ogv 1pcr 1pss 1pst 1qov 1rg5 1rgn 1rqk 1rvj 1ry5 1rzh 1rzz 1s00 1umx 1yf6 1yst 1z9j 1z9k 2bnp 2bns 2boz 2gmr 2gnu 2hg3 2hg9 2hh1 2hhk 2hit 2hj6 2j8c 2j8d 2jiy 2jj0 2rcr 2uws 2uwt 2uwu 2uwv 2uww 2ux3 2ux4 2ux5 2uxj 2uxk 2uxl 2uxm 2wx5 3dsy 3dta 3dtr 3dts 3du2 3du3 3duq 3i4d 3v3y 3v3z 3zum 3zuw 4h99 4h9l 4hbh 4hbj 4in5 4in6 4in7 4lwy 4n7k 4n7l 4tqq 4v9g 5lse 5v33

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4RCR)