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(-) Description

Title :  CRYSTAL STRUCTURE OF NEW TRIGONAL FORM OF PHOTOSYNTHETIC REACTION CENTER FROM BLASTOCHLORIS VIRIDIS. CRYSTALS GROWN IN MICROFLUIDICS BY DETERGENT CAPTURE.
 
Authors :  L. Li, S. H. M. Nachtergaele, A. M. Seddon, V. Tereshko, N. Ponomarenko, R. F. Ismagilov, Accelerated Technologies Center For Gene To 3 Structure (Atcg3D)
Date :  09 May 08  (Deposition) - 08 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.21
Chains :  Asym./Biol. Unit :  C,H,L,M
Keywords :  Detergent Extraction, Reaction Center, Microfludics, Plugs, Structural Genomics, Psi-2, Protein Structure Initiative, Accelerated Technologies Center For Gene To 3D Structure, Atcg3D, Electron Transport, Heme, Iron, Lipoprotein, Membrane, Metal- Binding, Photosynthesis, Transport, Bacteriochlorophyll, Chlorophyll, Chromophore, Formylation, Transmembrane, Magnesium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Li, S. Nachtergaele, A. M. Seddon, V. Tereshko, N. Ponomarenko, R. F. Ismagilov
Simple Host-Guest Chemistry To Modulate The Process Of Concentration And Crystallization Of Membrane Proteins By Detergent Capture In A Microfluidic Device.
J. Am. Chem. Soc. V. 130 14324 2008
PubMed-ID: 18831551  |  Reference-DOI: 10.1021/JA805361J

(-) Compounds

Molecule 1 - PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT
    Atcc: 19567
    Chains: C
    Organism Scientific: BLASTOCHLORIS VIRIDIS
    Organism Taxid: 1079
    Synonym: CYTOCHROME C558/C559
 
Molecule 2 - REACTION CENTER PROTEIN H CHAIN
    Atcc: 19567
    Chains: H
    Organism Scientific: BLASTOCHLORIS VIRIDIS
    Organism Taxid: 1079
    Synonym: PHOTOSYNTHETIC REACTION CENTER H SUBUNIT
 
Molecule 3 - REACTION CENTER PROTEIN L CHAIN
    Atcc: 19567
    Chains: L
    Organism Scientific: BLASTOCHLORIS VIRIDIS
    Organism Taxid: 1079
    Synonym: PHOTOSYNTHETIC REACTION CENTER L SUBUNIT
 
Molecule 4 - REACTION CENTER PROTEIN M CHAIN
    Atcc: 19567
    Chains: M
    Organism Scientific: BLASTOCHLORIS VIRIDIS
    Organism Taxid: 1079
    Synonym: PHOTOSYNTHETIC REACTION CENTER M SUBUNIT

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : CHLM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (11, 38)

Asymmetric/Biological Unit (11, 38)
No.NameCountTypeFull Name
1BCB4Ligand/IonBACTERIOCHLOROPHYLL B
2BPB2Ligand/IonBACTERIOPHEOPHYTIN B
3FE21Ligand/IonFE (II) ION
4FME1Mod. Amino AcidN-FORMYLMETHIONINE
5HEC4Ligand/IonHEME C
6HTO3Ligand/IonHEPTANE-1,2,3-TRIOL
7LDA4Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
8MQ91Ligand/IonMENAQUINONE-9
9NS51Ligand/Ion15-CIS-1,2-DIHYDRONEUROSPORENE
10SO415Ligand/IonSULFATE ION
11UQ12Ligand/IonUBIQUINONE-1

(-) Sites  (37, 37)

Asymmetric Unit (37, 37)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS L:190 , HIS L:230 , HIS M:217 , GLU M:232 , HIS M:264BINDING SITE FOR RESIDUE FE2 M 500
02AC2SOFTWAREASN L:199 , HIS M:143 , ARG M:265BINDING SITE FOR RESIDUE SO4 M 801
03AC3SOFTWARETRP M:23 , TYR M:50 , GLY M:52 , ALA M:53 , SER M:54 , SER M:133BINDING SITE FOR RESIDUE SO4 M 802
04AC4SOFTWARETHR H:250 , ARG H:253BINDING SITE FOR RESIDUE SO4 H 803
05AC5SOFTWARELEU H:246 , ALA M:1 , ARG M:226BINDING SITE FOR RESIDUE SO4 M 804
06AC6SOFTWARESER M:35 , TYR M:36 , TRP M:37BINDING SITE FOR RESIDUE SO4 M 805
07AC7SOFTWAREARG H:37 , TYR H:41 , GLU H:61 , ARG M:251BINDING SITE FOR RESIDUE SO4 H 806
08AC8SOFTWARETYR H:117 , GLU H:119 , ARG H:233 , LYS H:237BINDING SITE FOR RESIDUE SO4 H 807
09AC9SOFTWAREALA C:319 , SER C:320 , ARG C:321BINDING SITE FOR RESIDUE SO4 C 808
10BC1SOFTWAREGLU C:112 , ARG C:115BINDING SITE FOR RESIDUE SO4 C 809
11BC2SOFTWAREASN C:196 , LYS C:198 , ARG C:199BINDING SITE FOR RESIDUE SO4 C 810
12BC3SOFTWAREHIS C:162 , ARG C:165 , ASP L:70 , LYS L:72 , TYR L:73 , GLU L:82BINDING SITE FOR RESIDUE SO4 C 811
13BC4SOFTWAREHIS H:72 , ASP H:129BINDING SITE FOR RESIDUE SO4 H 812
14BC5SOFTWARETHR C:161 , HIS C:162 , LYS L:72BINDING SITE FOR RESIDUE SO4 C 813
15BC6SOFTWARELYS C:258 , ARG C:293BINDING SITE FOR RESIDUE SO4 C 814
16BC7SOFTWAREPRO C:160 , ARG C:165 , PRO M:306BINDING SITE FOR RESIDUE SO4 C 815
17BC8SOFTWARETYR C:56 , LYS C:57 , ASN C:58 , LYS C:60 , LEU C:62 , PHE C:70 , LEU C:71 , MET C:74 , THR C:75 , ILE C:77 , THR C:78 , CYS C:87 , CYS C:90 , HIS C:91 , LEU C:96 , ALA C:97 , TYR C:104 , ALA C:107 , ARG C:108BINDING SITE FOR RESIDUE HEC C 401
18BC9SOFTWARETYR C:89 , TYR C:102 , MET C:110 , LEU C:111 , MET C:113 , THR C:114 , THR C:131 , CYS C:132 , CYS C:135 , HIS C:136 , PRO C:140 , LEU C:141 , PRO C:142 , ARG C:293 , PRO C:301BINDING SITE FOR RESIDUE HEC C 402
19CC1SOFTWAREARG C:202 , PHE C:230 , MET C:233 , MET C:234 , ILE C:236 , SER C:237 , LEU C:240 , ASN C:243 , CYS C:244 , CYS C:247 , HIS C:248 , PHE C:253 , GLU C:254 , ARG C:264 , ALA C:267 , TRP C:268 , ARG C:272 , ILE M:189BINDING SITE FOR RESIDUE HEC C 403
20CC2SOFTWAREHIS C:124 , THR C:128 , ILE C:236 , LEU C:240 , PHE C:246 , GLN C:263 , ILE C:266 , GLY C:270 , ILE C:271 , MET C:273 , CYS C:305 , CYS C:308 , HIS C:309 , THR C:313 , LYS C:314 , PRO C:315BINDING SITE FOR RESIDUE HEC C 404
21CC3SOFTWAREPHE L:97 , PRO L:124 , MET L:127 , PHE L:128 , ASN L:158 , PHE L:160 , GLY L:161 , TYR L:162 , TRP L:167 , HIS L:168 , HIS L:173 , SER L:176 , ILE L:240 , PHE L:241 , GLY L:244 , THR L:248 , TYR M:195 , TYR M:208BINDING SITE FOR RESIDUE BCB L 400
22CC4SOFTWAREPHE L:128 , PHE L:146 , ILE L:150 , HIS L:153 , LEU L:154 , GLY M:201 , ILE M:204 , GLY M:205 , TYR M:208 , GLY M:209BINDING SITE FOR RESIDUE BCB L 401
23CC5SOFTWAREPHE L:41 , ILE L:42 , PHE L:97 , TRP L:100 , GLU L:104 , PHE L:121 , PRO L:124 , TYR L:148 , GLY L:149 , ILE L:150 , HIS L:153 , ALA L:237 , PHE L:241 , TYR M:208 , GLY M:211 , LEU M:212 , TRP M:250BINDING SITE FOR RESIDUE BPB L 402
24CC6SOFTWARETYR L:29 , ILE L:39 , PHE L:43 , TRP L:100 , HIS M:217 , ALA M:246 , TRP M:250 , ILE M:254 , ASN M:257 , ALA M:258 , TRP M:266BINDING SITE FOR RESIDUE MQ9 M 501
25CC7SOFTWARELEU L:189 , HIS L:190 , LEU L:193 , GLU L:212 , ASN L:213 , PHE L:216 , SER L:223 , ILE L:224 , GLY L:225 , ILE L:229BINDING SITE FOR RESIDUE UQ1 L 502
26CC8SOFTWARETRP L:266 , PHE M:85 , PHE M:88 , PHE M:89BINDING SITE FOR RESIDUE UQ1 L 503
27CC9SOFTWAREHIS L:168 , MET L:174 , SER L:178 , PHE L:181 , MET L:185 , ILE M:177 , TRP M:178 , HIS M:180 , ILE M:181 , LEU M:184BINDING SITE FOR RESIDUE BCB M 400
28DC1SOFTWARETYR L:162 , PHE L:181 , GLY M:62 , LEU M:124 , PHE M:154 , LEU M:184 , THR M:185 , PHE M:187 , SER M:188 , PHE M:194 , TYR M:195 , HIS M:200 , SER M:203 , ILE M:204 , TYR M:208 , MET M:275 , ALA M:278 , ILE M:282BINDING SITE FOR RESIDUE BCB M 401
29DC2SOFTWAREPHE L:181 , ALA L:184 , MET L:185 , LEU L:189 , ALA M:58 , PHE M:59 , SER M:123 , LEU M:124 , TRP M:127 , ILE M:144 , ASN M:147 , PHE M:148 , SER M:271BINDING SITE FOR RESIDUE BPB M 402
30DC3SOFTWARELEU M:70 , LEU M:114 , GLY M:117 , THR M:121 , GLY M:159 , CYS M:160 , PHE M:175 , GLY M:176 , ILE M:177 , HIS M:180BINDING SITE FOR RESIDUE NS5 M 600
31DC4SOFTWAREARG H:33 , ASP H:56BINDING SITE FOR RESIDUE LDA H 701
32DC5SOFTWARETRP H:17 , ASP L:60 , TYR M:195 , PRO M:198 , TRP M:295 , HIS M:299BINDING SITE FOR RESIDUE LDA L 702
33DC6SOFTWARELEU H:30 , ARG H:34 , TYR H:60 , LEU H:62 , TYR H:64BINDING SITE FOR RESIDUE LDA H 703
34DC7SOFTWAREALA M:53 , LEU M:122BINDING SITE FOR RESIDUE LDA M 704
35DC8SOFTWAREPRO H:71 , HIS H:72 , ASP H:125 , ALA H:126BINDING SITE FOR RESIDUE HTO H 705
36DC9SOFTWAREPRO C:205 , GLN C:206 , ARG C:221BINDING SITE FOR RESIDUE HTO C 706
37EC1SOFTWAREGLU C:21 , GLY C:241 , THR C:313BINDING SITE FOR RESIDUE HTO C 707

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D38)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Pro C:5 -Pro C:6
2Leu C:152 -Pro C:153
3Gly C:329 -Pro C:330
4Tyr H:41 -Pro H:42
5Val H:78 -Pro H:79
6Gly M:47 -Pro M:48

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D38)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.CYCR_BLAVI102-334  1C:82-314
2REACTION_CENTERPS00244 Photosynthetic reaction center proteins signature.RCEL_BLAVI167-193  1L:166-192
RCEM_BLAVI194-220  1M:193-219

(-) Exons   (0, 0)

(no "Exon" information available for 3D38)

(-) 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:332
 aligned with CYCR_BLAVI | P07173 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:332
                                    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       320       330       340       350  
           CYCR_BLAVI    21 CFEPPPATTTQTGFRGLSMGEVLHPATVKAKKERDAQYPPALAAVKAEGPPVSQVYKNVKVLGNLTEAEFLRTMTAITEWVSPQEGCTYCHDENNLASEAKYPYVVARRMLEMTRAINTNWTQHVAQTGVTCYTCHRGTPLPPYVRYLEPTLPLNNRETPTHVERVETRSGYVVRLAKYTAYSALNYDPFTMFLANDKRQVRVVPQTALPLVGVSRGKERRPLSDAYATFALMMSISDSLGTNCTFCHNAQTFESWGKKSTPQRAIAWWGIRMVRDLNMNYLAPLNASLPASRLGRQGEAPQADCRTCHQGVTKPLFGASRLKDYPELGPIK 352
               SCOP domains d3d38c1 C:1-332 Photosynthetic reaction centre (cytochrome subunit)                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -----------------------3d38C01 C:24-142,C:314-332 Photosynthetic Reaction Center, subunit C, domain 2                                         3d38C02 C:143-205,C:221-313                                    ---------------3d38C02 C:143-205,C:221-313 Photosynthetic Reaction Center, subunit C, domain 2              3d38C01             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee............eehhhhhhhhhhhhhhh............hhhhhh.........hhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhh.........hhhhhhh..............................hhhhhhhhhhh.........hhhhhhh.....................hhhhh..hhhhhhhhhhhhhhhhhhh.hhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...............hhhhhhh...hhhhhh.....hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------MULTIHEME_CYTC  PDB: C:82-314 UniProt: 102-334                                                                                                                                                                                           ------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d38 C   1 CFEPPPATTTQTGFRGLSMGEVLHPATVKAKKERDAQYPPALAAVKAEGPPVSQVYKNVKVLGNLTEAEFLRTMTAITEWVSPQEGCTYCHDENNLASEAKYPYVVARRMLEMTRAINTNWTQHVAQTGVTCYTCHRGTPLPPYVRYLEPTLPLNNRETPTHVERVETRSGYVVRLAKYTAYSALNYDPFTMFLANDKRQVRVVPQTALPLVGVSRGKERRPLSDAYATFALMMSISDSLGTNCTFCHNAQTFESWGKKSTPQRAIAWWGIRMVRDLNMNYLAPLNASLPASRLGRQGEAPQADCRTCHQGVTKPLFGASRLKDYPELGPIK 332
                                    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       320       330  


Chain H from PDB  Type:PROTEIN  Length:250
 aligned with RCEH_BLAVI | P06008 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:258
                                    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        
           RCEH_BLAVI     1 MYHGALAQHLDIAQLVWYAQWLVIWTVVLLYLRREDRREGYPLVEPLGLVKLAPEDGQVYELPYPKTFVLPHGGTVTVPRRRPETRELKLAQTDGFEGAPLQPTGNPLVDAVGPASYAERAEVVDATVDGKAKIVPLRVATDFSIAEGDVDPRGLPVVAADGVEAGTVTDLWVDRSEHYFRYLELSVAGSARTALIPLGFCDVKKDKIVVTSILSEQFANVPRLQSRDQITLREEDKVSAYYAGGLLYATPERAESLL 258
               SCOP domains d3d38h2 H:1-36                      d3d38h1 H        :37-258 Photosynthetic reaction centre                                                                                                                                                                        SCOP domains
               CATH domains -3d38H01 H:2-119 Photosynthetic Reaction Cent        er, subunit H, domain 1                                           3d38H02 H:120-258 Photosynthetic Reaction Center, subunit H, domain 2                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee...eehhhhhhhhhhhhhhhhhhhhhhhhh.........--------..hhhhhh....eeee.....eeee...........eee........eee..hhhhhhhhhhh.................eee.......ee..........eee.....eeeeeeeeeee....eeeeeeeee....eeeeee.hhhee....ee....hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3d38 H   1 mYHGALAQHLDIAQLVWYAQWLVIWTVVLLYLRREDRREGYPLVE--------PEDGQVYELPYPKTFVLPHGGTVTVPRRRPETRELKLAQTDGFEGAPLQPTGNPLVDAVGPASYAERAEVVDATVDGKAKIVPLRVATDFSIAEGDVDPRGLPVVAADGVEAGTVTDLWVDRSEHYFRYLELSVAGSARTALIPLGFCDVKKDKIVVTSILSEQFANVPRLQSRDQITLREEDKVSAYYAGGLLYATPERAESLL 258
                            |       10        20        30        40    |    -   |    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250        
                            1-FME                                      45       54                                                                                                                                                                                                            


Chain L from PDB  Type:PROTEIN  Length:273
 aligned with RCEL_BLAVI | P06009 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:273
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271   
           RCEL_BLAVI     2 ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNIFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS 274
               SCOP domains d3d38l1 L:1-273 L (light) subunit                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3d38L01 L:1-165 Membrane spanning alpha-helix pairs                                                                                                                  3d38L02 L:166-273 Membrane spanning alpha-helix pairs                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.......hhhhhh.ee..eehhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------REACTION_CENTER            --------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d38 L   1 ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNIFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS 273
                                    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   


Chain M from PDB  Type:PROTEIN  Length:323
 aligned with RCEM_BLAVI | P06010 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:323
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   
           RCEM_BLAVI     2 ADYQTIYTQIQARGPHITVSGEWGDNDRVGKPFYSYWLGKIGDAQIGPIYLGASGIAAFAFGSTAILIILFNMAAEVHFDPLQFFRQFFWLGLYPPKAQYGMGIPPLHDGGWWLMAGLFMTLSLGSWWIRVYSRARALGLGTHIAWNFAAAIFFVLCIGCIHPTLVGSWSEGVPFGIWPHIDWLTAFSIRYGNFYYCPWHGFSIGFAYGCGLLFAAHGATILAVARFGGDREIEQITDRGTAVERAALFWRWTIGFNATIESVHRWGWFFSLMVMVSASVGILLTGTFVDNWYLWCVKHGAAPDYPAYLPATPDPASLPGAPK 324
               SCOP domains d3d38m1 M:1-323 M (medium) subunit                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3d38M01 M:1-143 Membrane spanning alpha-helix pairs                                                                                            3d38M02 M:144-302 Membrane spanning alpha-helix pairs                                                                                                          --------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....ee..............ee.......hhhhh.......ee.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..............hhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------REACTION_CENTER            -------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d38 M   1 ADYQTIYTQIQARGPHITVSGEWGDNDRVGKPFYSYWLGKIGDAQIGPIYLGASGIAAFAFGSTAILIILFNMAAEVHFDPLQFFRQFFWLGLYPPKAQYGMGIPPLHDGGWWLMAGLFMTLSLGSWWIRVYSRARALGLGTHIAWNFAAAIFFVLCIGCIHPTLVGSWSEGVPFGIWPHIDWLTAFSIRYGNFYYCPWHGFSIGFAYGCGLLFAAHGATILAVARFGGDREIEQITDRGTAVERAALFWRWTIGFNATIESVHRWGWFFSLMVMVSASVGILLTGTFVDNWYLWCVKHGAAPDYPAYLPATPDPASLPGAPK 323
                                    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       320
   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  (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 3D38)

(-) Gene Ontology  (17, 47)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C   (CYCR_BLAVI | P07173)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
    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: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.
    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.

Chain H   (RCEH_BLAVI | P06008)
molecular function
    GO:0042314    bacteriochlorophyll binding    Interacting selectively and non-covalently with bacteriochlorophyll, a form of chlorophyll found in photosynthetic bacteria, such as the purple and green bacteria. There are several types, designated a to g. Bacteriochlorophyll a and bacteriochlorophyll b are structurally similar to the chlorophyll a and chlorophyll b found in plants.
    GO:0016168    chlorophyll binding    Interacting selectively and non-covalently with chlorophyll; any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment.
    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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
    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.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
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.
    GO:0042717    plasma membrane-derived chromatophore membrane    The lipid bilayer associated with a plasma membrane-derived chromatophore; surrounds chromatophores that form complete vesicles.

Chain L   (RCEL_BLAVI | P06009)
molecular function
    GO:0042314    bacteriochlorophyll binding    Interacting selectively and non-covalently with bacteriochlorophyll, a form of chlorophyll found in photosynthetic bacteria, such as the purple and green bacteria. There are several types, designated a to g. Bacteriochlorophyll a and bacteriochlorophyll b are structurally similar to the chlorophyll a and chlorophyll b found in plants.
    GO:0016168    chlorophyll binding    Interacting selectively and non-covalently with chlorophyll; any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment.
    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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
    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.
    GO:0009772    photosynthetic electron transport in photosystem II    A photosynthetic electron transport chain in which electrons move from the primary electron acceptor (Quinone, Q) through a chain of electron transport molecules in the thylakoid membrane until they reach the ultimate electron acceptor of Photosystem II, which is plastocyanin (PC). The electron is then passed to the P700 chlorophyll a molecules of the reaction centre of photosystem I.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
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.
    GO:0042717    plasma membrane-derived chromatophore membrane    The lipid bilayer associated with a plasma membrane-derived chromatophore; surrounds chromatophores that form complete vesicles.

Chain M   (RCEM_BLAVI | P06010)
molecular function
    GO:0042314    bacteriochlorophyll binding    Interacting selectively and non-covalently with bacteriochlorophyll, a form of chlorophyll found in photosynthetic bacteria, such as the purple and green bacteria. There are several types, designated a to g. Bacteriochlorophyll a and bacteriochlorophyll b are structurally similar to the chlorophyll a and chlorophyll b found in plants.
    GO:0016168    chlorophyll binding    Interacting selectively and non-covalently with chlorophyll; any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment.
    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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
    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.
    GO:0009772    photosynthetic electron transport in photosystem II    A photosynthetic electron transport chain in which electrons move from the primary electron acceptor (Quinone, Q) through a chain of electron transport molecules in the thylakoid membrane until they reach the ultimate electron acceptor of Photosystem II, which is plastocyanin (PC). The electron is then passed to the P700 chlorophyll a molecules of the reaction centre of photosystem I.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
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.
    GO:0042717    plasma membrane-derived chromatophore membrane    The lipid bilayer associated with a plasma membrane-derived chromatophore; surrounds chromatophores that form complete vesicles.

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  3d38
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  CYCR_BLAVI | P07173
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 Related Entries

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

UniProtKB/Swiss-Prot
        CYCR_BLAVI | P07173: 1dxr 1prc 1r2c 1vrn 2i5n 2jbl 2prc 2wjm 2wjn 2x5u 2x5v 3g7f 3prc 3t6d 3t6e 4ac5 4cas 5m7j 5m7k 5m7l 5prc 6prc 7prc
        RCEH_BLAVI | P06008: 1dxr 1prc 1r2c 1vrn 2i5n 2jbl 2prc 2wjm 2wjn 2x5u 2x5v 3g7f 3prc 3t6d 3t6e 4ac5 4cas 5m7j 5m7k 5m7l 5prc 6prc 7prc
        RCEL_BLAVI | P06009: 1dxr 1prc 1r2c 1vrn 2i5n 2jbl 2prc 2wjm 2wjn 2x5u 2x5v 3g7f 3prc 3t6d 3t6e 4ac5 4cas 5m7j 5m7k 5m7l 5prc 6prc 7prc
        RCEM_BLAVI | P06010: 1dxr 1prc 1r2c 1vrn 2i5n 2jbl 2prc 2wjm 2wjn 2x5u 2x5v 3g7f 3prc 3t6d 3t6e 4ac5 4cas 5m7j 5m7k 5m7l 5prc 6prc 7prc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3D38)