6KMX

Structure of PSI from H. hongdechloris grown under far-red light condition


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for the adaptation and function of chlorophyll f in photosystem I

Kato, K.Shinoda, T.Nagao, R.Akimoto, S.Suzuki, T.Dohmae, N.Chen, M.Allakhverdiev, S.I.Shen, J.R.Akita, F.Miyazaki, N.Tomo, T.

(2020) Nat Commun --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem I P700 chlorophyll a apoprotein A1
aA, bA, cA
784Halomicronema hongdechloris C2206Mutation(s): 0 
Gene Names: psaA_1 (psaA)
EC: 1.97.1.12
Find proteins for A0A1Z3HIN6 (Halomicronema hongdechloris C2206)
Go to UniProtKB:  A0A1Z3HIN6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem I P700 chlorophyll a apoprotein A2
aB, bB, cB
743Halomicronema hongdechloris C2206Mutation(s): 0 
Gene Names: psaB_1 (psaB)
EC: 1.97.1.12
Find proteins for A0A1Z3HIL0 (Halomicronema hongdechloris C2206)
Go to UniProtKB:  A0A1Z3HIL0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem I iron-sulfur center
aC, bC, cC
81Halomicronema hongdechloris C2206Mutation(s): 0 
Gene Names: psaC
EC: 1.97.1.12
Find proteins for A0A1Z3HPE3 (Halomicronema hongdechloris C2206)
Go to UniProtKB:  A0A1Z3HPE3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit II
aD, bD, cD
142Halomicronema hongdechloris C2206Mutation(s): 0 
Gene Names: psaD
EC: 1.97.1.12
Find proteins for A0A1Z3HHI7 (Halomicronema hongdechloris C2206)
Go to UniProtKB:  A0A1Z3HHI7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit IV
aE, bE, cE
68Halomicronema hongdechloris C2206Mutation(s): 0 
Gene Names: psaE
Find proteins for A0A1Z3HI16 (Halomicronema hongdechloris C2206)
Go to UniProtKB:  A0A1Z3HI16
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit VIII
aI, bI, cI
63Halomicronema hongdechloris C2206Mutation(s): 0 
Gene Names: psaI_2
EC: 1.97.1.12
Find proteins for A0A1Z3HIL5 (Halomicronema hongdechloris C2206)
Go to UniProtKB:  A0A1Z3HIL5
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit PsaK
aK, bK, cK
96Halomicronema hongdechloris C2206Mutation(s): 0 
Gene Names: psaK
Find proteins for A0A1Z3HR36 (Halomicronema hongdechloris C2206)
Go to UniProtKB:  A0A1Z3HR36
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit XI
aL, bL, cL
189Halomicronema hongdechloris C2206Mutation(s): 0 
Gene Names: psaL_1
EC: 1.97.1.12
Find proteins for A0A1Z3HIQ7 (Halomicronema hongdechloris C2206)
Go to UniProtKB:  A0A1Z3HIQ7
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit XII
aM, bM, cM
31N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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aA, aC, bA, bC, cA, cC
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PQN
Query on PQN

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aA, aB, bA, bB, cA, cB
PHYLLOQUINONE
VITAMIN K1; 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
 Ligand Interaction
CLA
Query on CLA

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aA, aB, aK, aL, bA, bB, bK, bL, cA, cB, cK, cL
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
CL0
Query on CL0

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aA, bA, cA
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
 Ligand Interaction
F6C
Query on F6C

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Download CCD File 
aA, aB, aL, bA, bB, bL, cA, cB, cL
Chlorophyll F
[methyl 9-ethenyl-14-ethyl-8-formyl-4,13,18-trimethyl-20-oxo-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,23,25-tetradehydro-24,26-dihydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]magnesium
C55 H68 Mg N4 O6
YUTLCKLMRUVWDE-FOFJUSMOSA-M
 Ligand Interaction
CA
Query on CA

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aL, bL, cL
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
LMG
Query on LMG

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aB, bB, cB
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
BCR
Query on BCR

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Download CCD File 
aA, aB, aI, aK, aL, aM, bA, bB, bI, bK, bL, bM, cA, cB, cI, cK, cL, cM
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT
Query on LMT

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Download CCD File 
aA, bA, cA
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
LHG
Query on LHG

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Download CCD File 
aA, bA, cA
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-15
    Type: Initial release