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(-) Description

Title :  CRYSTAL STRUCTURE OF CYTOCHROME B6F IN DOPG, WITH DISORDERED RIESKE IRON-SULFUR PROTEIN SOLUBLE DOMAIN
 
Authors :  S. S. Hasan, J. T. Stofleth, E. Yamashita, W. A. Cramer
Date :  01 Dec 12  (Deposition) - 17 Apr 13  (Release) - 04 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D,E,F,G,H  (2x)
Keywords :  Cytochrome, Membrane Protein, Plastoquinol:Plastocyanin Oxidoreductase, Plastocyanin, Thylakoid Membrane, Photosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. S. Hasan, J. T. Stofleth, E. Yamashita, W. A. Cramer
Lipid-Induced Conformational Changes Within The Cytochrome B6F Complex Of Oxygenic Photosynthesis.
Biochemistry V. 52 2649 2013
PubMed-ID: 23514009  |  Reference-DOI: 10.1021/BI301638H

(-) Compounds

Molecule 1 - CYTOCHROME B6
    Chains: A
    Organism Scientific: MASTIGOCLADUS LAMINOSUS
    Organism Taxid: 83541
 
Molecule 2 - CYTOCHROME B6-F COMPLEX SUBUNIT 4
    Chains: B
    Organism Scientific: MASTIGOCLADUS LAMINOSUS
    Organism Taxid: 83541
    Synonym: 17 KDA POLYPEPTIDE
 
Molecule 3 - APOCYTOCHROME F
    Chains: C
    Fragment: UNP RESIDUES 45-333
    Organism Scientific: MASTIGOCLADUS LAMINOSUS
    Organism Taxid: 83541
 
Molecule 4 - CYTOCHROME B6-F COMPLEX IRON-SULFUR SUBUNIT
    Chains: D
    EC Number: 1.10.9.1
    Organism Scientific: MASTIGOCLADUS LAMINOSUS
    Organism Taxid: 83541
 
Molecule 5 - CYTOCHROME B6-F COMPLEX SUBUNIT 6
    Chains: E
    Organism Scientific: MASTIGOCLADUS LAMINOSUS
    Organism Taxid: 83541
    Synonym: CYTOCHROME B6-F COMPLEX SUBUNIT PETL, CYTOCHROME B6-F COMPLEX SUBUNIT VI
 
Molecule 6 - CYTOCHROME B6-F COMPLEX SUBUNIT 7
    Chains: F
    Organism Scientific: MASTIGOCLADUS LAMINOSUS
    Organism Taxid: 83541
    Synonym: CYTOCHROME B6-F COMPLEX SUBUNIT PETM, CYTOCHROME B6-F COMPLEX SUBUNIT VII
 
Molecule 7 - CYTOCHROME B6-F COMPLEX SUBUNIT 5
    Chains: G
    Organism Scientific: MASTIGOCLADUS LAMINOSUS
    Organism Taxid: 83541
    Synonym: CYTOCHROME B6-F COMPLEX SUBUNIT PETG, CYTOCHROME B6-F COMPLEX SUBUNIT V
 
Molecule 8 - CYTOCHROME B6-F COMPLEX SUBUNIT 8
    Chains: H
    Organism Scientific: MASTIGOCLADUS LAMINOSUS
    Organism Taxid: 83541
    Synonym: CYTOCHROME B6-F COMPLEX SUBUNIT PETN, CYTOCHROME B6-F COMPLEX SUBUNIT VIII

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (2x): ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 19)

Asymmetric Unit (10, 19)
No.NameCountTypeFull Name
11E21Ligand/Ion(2S)-3-(ACETYLOXY)-2-HYDROXYPROPYL 6-DEOXY-6-SULFO-BETA-D-GLUCOPYRANOSIDE
28K61Ligand/IonOCTADECANE
3BCR1Ligand/IonBETA-CAROTENE
4CD3Ligand/IonCADMIUM ION
5CLA1Ligand/IonCHLOROPHYLL A
6HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
7MYS1Ligand/IonPENTADECANE
8OCT1Ligand/IonN-OCTANE
9OZ23Ligand/Ion(2R)-3-{[(R)-{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6Z)-TRIDEC-6-ENOYLOXY]PROPYL (9Z)-OCTADEC-9-ENOATE
10UMQ3Ligand/IonUNDECYL-MALTOSIDE
Biological Unit 1 (9, 32)
No.NameCountTypeFull Name
11E22Ligand/Ion(2S)-3-(ACETYLOXY)-2-HYDROXYPROPYL 6-DEOXY-6-SULFO-BETA-D-GLUCOPYRANOSIDE
28K62Ligand/IonOCTADECANE
3BCR2Ligand/IonBETA-CAROTENE
4CD-1Ligand/IonCADMIUM ION
5CLA2Ligand/IonCHLOROPHYLL A
6HEM8Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
7MYS2Ligand/IonPENTADECANE
8OCT2Ligand/IonN-OCTANE
9OZ26Ligand/Ion(2R)-3-{[(R)-{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6Z)-TRIDEC-6-ENOYLOXY]PROPYL (9Z)-OCTADEC-9-ENOATE
10UMQ6Ligand/IonUNDECYL-MALTOSIDE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:47 , PHE A:48 , GLY A:51 , PHE A:52 , MET A:54 , TYR A:58 , ARG A:83 , HIS A:86 , ARG A:87 , ALA A:90 , THR A:128 , PHE A:131 , GLY A:135 , LEU A:138 , PRO A:139 , HIS A:187 , PHE A:189BINDING SITE FOR RESIDUE HEM A 301
02AC2SOFTWARETYR A:34 , GLY A:37 , GLY A:38 , THR A:40 , MET A:93 , HIS A:100 , VAL A:101 , ARG A:103 , VAL A:104 , GLY A:109 , ARG A:114 , THR A:117 , TRP A:118 , GLY A:121 , MET A:199 , HIS A:202 , PHE A:203 , ILE A:206 , ILE A:211 , SER A:212 , HEM A:303 , HOH A:401 , HOH A:402 , HOH A:403BINDING SITE FOR RESIDUE HEM A 302
03AC3SOFTWARETYR A:34 , CYS A:35 , GLY A:38 , THR A:42 , ILE A:206 , ARG A:207 , GLY A:210 , ILE A:211 , HEM A:302 , HOH A:401 , ASN B:25 , ASP B:35 , PHE B:40 , ILE B:44 , ARG H:26BINDING SITE FOR RESIDUE HEM A 303
04AC4SOFTWARELEU A:169 , ALA A:186BINDING SITE FOR RESIDUE MYS A 304
05AC5SOFTWAREPHE A:52 , MET A:199BINDING SITE FOR RESIDUE 8K6 A 305
06AC6SOFTWARELEU A:12 , GLU A:13 , ALA A:16 , LEU A:17 , ILE A:119 , LEU A:204 , LYS A:208BINDING SITE FOR RESIDUE UMQ A 306
07AC7SOFTWARETYR A:5 , ASP A:6 , ILE A:14 , GLN A:15 , ALA A:18 , UMQ A:308BINDING SITE FOR RESIDUE UMQ A 307
08AC8SOFTWAREALA A:18 , UMQ A:307 , GLU C:286 , 1E2 D:201BINDING SITE FOR RESIDUE UMQ A 308
09AC9SOFTWAREGLU A:75 , HIS C:143 , HOH C:401BINDING SITE FOR RESIDUE CD A 309
10BC1SOFTWARETYR A:105 , ALA A:125 , VAL A:129 , TYR B:80 , PRO B:83 , VAL B:84 , ILE B:87 , MET B:101 , ILE B:132 , PHE B:133 , GLY B:136 , VAL B:139 , THR B:140 , OZ2 B:203 , HOH B:301 , HOH B:302BINDING SITE FOR RESIDUE CLA B 201
11BC2SOFTWAREASP B:58 , LYS C:146 , GLU F:4 , GLU G:3BINDING SITE FOR RESIDUE CD B 202
12BC3SOFTWARETYR A:105 , SER B:103 , GLU B:115 , ASN B:118 , ARG B:126 , VAL B:128 , ALA B:129 , CLA B:201BINDING SITE FOR RESIDUE OZ2 B 203
13BC4SOFTWARETYR C:1 , TRP C:4 , ALA C:5 , CYS C:22 , CYS C:25 , HIS C:26 , GLN C:60 , LEU C:70 , ASN C:71 , VAL C:72 , GLY C:73 , ALA C:74 , ASN C:154 , GLY C:156 , ARG C:157 , GLY C:158 , ILE C:160 , TYR C:161BINDING SITE FOR RESIDUE HEM C 301
14BC5SOFTWAREHIS C:150BINDING SITE FOR RESIDUE CD C 302
15BC6SOFTWAREPHE A:78 , TRP A:80 , ASN C:253 , TRP C:257BINDING SITE FOR RESIDUE OZ2 C 303
16BC7SOFTWAREUMQ A:308 , TRP B:32 , PRO B:33 , TYR B:38 , LYS C:275 , VAL C:279 , ARG D:16 , ASN D:20 , PHE D:24BINDING SITE FOR RESIDUE 1E2 D 201
17BC8SOFTWAREILE A:32 , PHE A:33 , ILE A:39 , MET A:96 , LEU A:99 , ILE F:16 , PHE F:17 , ALA G:16 , GLY G:19 , GLY G:20 , TYR G:23 , OZ2 G:102 , ILE H:19BINDING SITE FOR RESIDUE BCR G 101
18BC9SOFTWAREMET A:92 , PRO C:37 , GLN C:38 , TYR E:8 , TYR F:7 , LEU G:5 , LEU G:9 , BCR G:101 , TRP H:8 , LEU H:12 , PHE H:15BINDING SITE FOR RESIDUE OZ2 G 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I7Z)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:112 -Pro A:113
2Trp B:32 -Pro B:33
3Gly C:117 -Pro C:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I7Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I7Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4I7Z)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains d4i7za_ A: automated matches                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhee....hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i7z A   3 NVYDWFQERLEIQALADDVTSKYVPPHVNIFYCLGGITLTCFLIQFATGFAMTFYYKPTVTEAYASVQYIMNEVSFGWLIRSIHRWSASMMVLMMILHVFRVYLTGGFKKPRELTWISGVILAVITVSFGVTGYSLPWDQVGYWAVKIVSGVPEAIPVVGVLISDLLRGGSSVGQATLTRYYSAHTFVLPWLIAVFMLLHFLMIRKQGISGPL 215
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212   


Chain B from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains d4i7zb_ B: Subunit IV of the cytochrome b6f complex                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhh........ee........hhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i7z B   2 ATLKKPDLSDPKLRAKLAKGMGHNYYGEPAWPNDLLYVFPVVIMGTFACIVALSVLDPAMVGEPADPFATPLEILPEWYLYPVFQILRSVPNKLLGVLLMASVPLGLILVPFIENVNKFQNPFRRPVATTIFLFGTLVTIWLGIGATFPLDKTLTLGLF 160
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151         


Chain C from PDB  Type:PROTEIN  Length:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4i7zc1 C:1-169,C:232-249 Cytochrome f, large domain                                                                                                                     d4i7zc2 C:170-231 Cytochrome f, small domain                  d4i7zc1           d4i7zc3 C:250-288                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh..........hhhhhh.......eee...ee....eeeeeee........ee.....ee..eeeeeee.....ee.hhhhhhhhhhhhhh....ee.......eeeeeeee.....eeeeeee............eeeeeeeeeee......................................ee...............ee..........................eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4i7z C   1 YPFWAQQTYPPTPREPTGRIVCANCHLAAKPAEVEVPQSVLPDTVFKAVVKIPYDTKLQQVAADGSKVGLNVGAVLMLPEGFKIAPEERIPEELKKEVGDVYFQPYKEGQDNVLLVGPLPGEQYQEIVFPVLSPNPTTDKNIHFGKYAIHLGANRGRGQIYPTGEKSNNNVFTASATGTITKIAKEEDEYGNVKYQVSIQTDSGKTVVDTIPAGPELIVSEGQAVKAGEALTNNPNVGGFGQDDTEIVLQDPNRVKWMIAFICLVMLAQLMLILKKKQVEKVQAAEMN 288
                                    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 D from PDB  Type:PROTEIN  Length:38
                                                                      
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 4i7z D   9 DVPDMGRRQFMNLLAFGTVTGVALGALYPLVKYFIPPS  46
                                    18        28        38        


Chain E from PDB  Type:PROTEIN  Length:28
                                                            
               SCOP domains d4i7ze_ E:                   SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                 4i7z E   2 ILGAVFYIVFIALFFGIAVGIIFAIKSI  29
                                    11        21        


Chain F from PDB  Type:PROTEIN  Length:31
                                                               
               SCOP domains d4i7zf_ F:                      SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                 4i7z F   2 TEEMLYAALLSFGLIFVGWGLGVLLLKIQGA  32
                                    11        21        31 


Chain G from PDB  Type:PROTEIN  Length:35
                                                                   
               SCOP domains d4i7zg_ G: automated matches        SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                 4i7z G   3 EPLLDGLVLGLVFATLGGLFYAAYQQYKRPNELGG  37
                                    12        22        32     


Chain H from PDB  Type:PROTEIN  Length:28
                                                            
               SCOP domains d4i7zh_ H: automated matches SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                 4i7z H   2 EIDVLGWVALLVVFTWSIAMVVWGRNGL  29
                                    11        21
   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  (9, 9)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)
(-)
Fold: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) (46)
(-)
Fold: Heme-binding four-helical bundle (113)
(-)
Fold: Single transmembrane helix (568)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I7Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I7Z)

(-) Gene Ontology  (23, 85)

Asymmetric Unit(hide GO term definitions)

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  4i7z
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  CYB6_MASLA | P83791
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  CYF_MASLA | P83793
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  PETD_MASLA | P83792
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  PETG_MASLA | P83797
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    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
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Access by UniProt ID/Accession number
  CYB6_MASLA | P83791
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CYF_MASLA | P83793
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PETD_MASLA | P83792
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PETG_MASLA | P83797
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PETL_MASLA | P83795
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PETM_MASLA | P83796
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PETN_MASLA | P83798
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  UCRI_MASLA | P83794
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CYB6_MASLA | P83791: 1vf5 2d2c 2e74 2e75 2e76 4h0l 4h13 4pv1
        CYF_MASLA | P83793: 1vf5 2d2c 2e74 2e75 2e76 4h0l 4h13 4pv1
        PETD_MASLA | P83792: 1vf5 2d2c 2e74 2e75 2e76 4h0l 4h13 4pv1
        PETG_MASLA | P83797: 1vf5 2d2c 2e74 2e75 2e76 4h0l 4h13 4pv1
        PETL_MASLA | P83795: 1vf5 2d2c 2e74 2e75 2e76 4h0l 4h13 4pv1
        PETM_MASLA | P83796: 1vf5 2d2c 2e74 2e75 2e76 4h0l 4h13 4pv1
        PETN_MASLA | P83798: 1vf5 2d2c 2e74 2e75 2e76 4h0l 4h13 4pv1
        UCRI_MASLA | P83794: 1vf5 2d2c 2e74 2e75 2e76 4h0l 4h13 4pv1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4I7Z)