2ZT9

Crystal Structure of the Cytochrome b6f Complex from Nostoc sp. PCC 7120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure-Function, Stability, and Chemical Modification of the Cyanobacterial Cytochrome b6f Complex from Nostoc sp. PCC 7120

Baniulis, D.Yamashita, E.Whitelegge, J.P.Zatsman, A.I.Hendrich, M.P.Hasan, S.S.Ryan, C.M.Cramer, W.A.

(2009) J Biol Chem 284: 9861-9869

  • DOI: 10.1074/jbc.M809196200
  • Primary Citation of Related Structures:  
    2ZT9

  • PubMed Abstract: 
  • The crystal structure of the cyanobacterial cytochrome b(6)f complex has previously been solved to 3.0-A resolution using the thermophilic Mastigocladus laminosus whose genome has not been sequenced. Several unicellular cyanobacteria, whose genomes have been sequenced and are tractable for mutagenesis, do not yield b(6)f complex in an intact dimeric state with significant electron transport activity ...

    The crystal structure of the cyanobacterial cytochrome b(6)f complex has previously been solved to 3.0-A resolution using the thermophilic Mastigocladus laminosus whose genome has not been sequenced. Several unicellular cyanobacteria, whose genomes have been sequenced and are tractable for mutagenesis, do not yield b(6)f complex in an intact dimeric state with significant electron transport activity. The genome of Nostoc sp. PCC 7120 has been sequenced and is closer phylogenetically to M. laminosus than are unicellular cyanobacteria. The amino acid sequences of the large core subunits and four small peripheral subunits of Nostoc are 88 and 80% identical to those in the M. laminosus b(6)f complex. Purified b(6)f complex from Nostoc has a stable dimeric structure, eight subunits with masses similar to those of M. laminosus, and comparable electron transport activity. The crystal structure of the native b(6)f complex, determined to a resolution of 3.0A (PDB id: 2ZT9), is almost identical to that of M. laminosus. Two unique aspects of the Nostoc complex are: (i) a dominant conformation of heme b(p) that is rotated 180 degrees about the alpha- and gamma-meso carbon axis relative to the orientation in the M. laminosus complex and (ii) acetylation of the Rieske iron-sulfur protein (PetC) at the N terminus, a post-translational modification unprecedented in cyanobacterial membrane and electron transport proteins, and in polypeptides of cytochrome bc complexes from any source. The high spin electronic character of the unique heme c(n) is similar to that previously found in the b(6)f complex from other sources.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6A215Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: petBalr3421
Membrane Entity: Yes 
UniProt
Find proteins for P0A384 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore P0A384 
Go to UniProtKB:  P0A384
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 4B160Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: petDalr3422
Membrane Entity: Yes 
UniProt
Find proteins for Q93SX1 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Apocytochrome fC289Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: petAall2452
Membrane Entity: Yes 
UniProt
Find proteins for Q93SW9 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex iron-sulfur subunit 1D179Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: petC1all2453
EC: 1.10.99.1 (PDB Primary Data), 7.1.1.6 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q93SX0 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 6E31Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: petLasl1922
Membrane Entity: Yes 
UniProt
Find proteins for Q8YVQ2 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 7F34Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: petMasl4754
Membrane Entity: Yes 
UniProt
Find proteins for P0A3Y1 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 5G37Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: petGasr1366
Membrane Entity: Yes 
UniProt
Find proteins for P58246 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 8H29Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: petNasl4263
Membrane Entity: Yes 
UniProt
Find proteins for P61048 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

Download Ideal Coordinates CCD File 
O [auth B]CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
OPC
Query on OPC

Download Ideal Coordinates CCD File 
P [auth B], U [auth H](7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE
C45 H87 N O8 P
CTQFGTDUPDRLRZ-CNMUNUSJSA-O
 Ligand Interaction
SQD
Query on SQD

Download Ideal Coordinates CCD File 
Q [auth B]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
HEM
Query on HEM

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], K [auth A], R [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR

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T [auth G]BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
UMQ
Query on UMQ

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L [auth A], M [auth A], N [auth A]UNDECYL-MALTOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
S [auth D]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.225α = 90
b = 159.225β = 90
c = 365.886γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2013-12-11
    Changes: Database references
  • Version 1.3: 2018-06-20
    Changes: Data collection, Structure summary
  • Version 1.4: 2019-10-02
    Changes: Advisory, Data collection, Derived calculations