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38  structures 270  species 0  interactions 423  sequences 29  architectures

Family: Apocytochr_F_C (PF01333)

Summary: Apocytochrome F, C-terminal

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This is the Wikipedia entry entitled "Cytochrome f". More...

Cytochrome f Edit Wikipedia article

PDB 1ci3 EBI.jpg
cytochrome f from the b6f complex of Phormidium laminosum
Pfam clanCL0105
OPM superfamily92
OPM protein3h1j

Cytochrome f is the largest subunit of cytochrome b6f complex (plastoquinol—plastocyanin reductase; EC In its structure and functions, the cytochrome b6f complex bears extensive analogy to the cytochrome bc1 complex of mitochondria and photosynthetic purple bacteria. Cytochrome f (cyt f) plays a role analogous to that of cytochrome c1, in spite of their different structures.[1]

The 3D structure of Brassica rapa (Turnip) cyt f has been determined.[2] The lumen-side segment of cyt f includes two structural domains: a small one above a larger one that, in turn, is on top of the attachment to the membrane domain. The large domain consists of an anti-parallel beta-sandwich and a short haem-binding peptide, which form a three-layer structure. The small domain is inserted between beta-strands F and G of the large domain and is an all-beta domain. The haem nestles between two short helices at the N terminus of cyt f. Within the second helix is the sequence motif for the c-type cytochromes, CxxCH (residues 21-25), which is covalently attached to the haem through thioether bonds to Cys-21 and Cys-24. His-25 is the fifth haem iron ligand. The sixth haem iron ligand is the alpha-amino group of Tyr-1 in the first helix.[2] Cyt f has an internal network of water molecules that may function as a proton wire.[2] The water chain appears to be a conserved feature of cyt f.


  1. ^ Prince RC, George GN (June 1995). "Cytochrome f revealed". Trends Biochem. Sci. 20 (6): 217–8. doi:10.1016/S0968-0004(00)89018-0. PMID 7631417.
  2. ^ a b c Martinez SE, Huang D, Ponomarev M, Cramer WA, Smith JL (June 1996). "The heme redox center of chloroplast cytochrome f is linked to a buried five-water chain". Protein Sci. 5 (6): 1081–92. doi:10.1002/pro.5560050610. PMC 2143431. PMID 8762139.

Further reading

External links

This article incorporates text from the public domain Pfam and InterPro: IPR002325

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Apocytochrome F, C-terminal Provide feedback

This is a sub-family of cytochrome C. See PF00034.

Literature references

  1. Martinez SE, Huang D, Szczepaniak A, Cramer WA, Smith JL; , Structure 1994;2:95-105.: Crystal structure of chloroplast cytochrome f reveals a novel cytochrome fold and unexpected heme ligation. PUBMED:8081747 EPMC:8081747

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002325

The cytochrome b6f integral membrane protein complex transfers electrons between the two reaction centre complexes of oxygenic photosynthetic membranes, and participates in formation of the transmembrane electrochemical proton gradient by also transferring protons from the stromal to the internal lumen compartment. The cytochrome b6f complex contains four polypeptides: cytochrome f (285 aa); cytochrome b6 (215 aa); Rieske iron-sulphur protein (179 aa); and subunit IV (160 aa) [ PUBMED:8027021 ]. In its structure and functions, the cytochrome b6f complex bears extensive analogy to the cytochrome bc1 complex of mitochondria and photosynthetic purple bacteria; cytochrome f (cyt f) plays a role analogous to that of cytochrome c1, in spite of their different structures [ PUBMED:7631417 ].

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Hybrid (CL0105), which has the following description:

This superfamily contains proteins with a hybrid motif [1]. This motif is embedded in structurally diverse proteins.

The clan contains the following 26 members:

Apocytochr_F_C Biotin_carb_C Biotin_lipoyl Biotin_lipoyl_2 Complex1_51K CusB_dom_1 DUF2118 DUF2254 GARS_C GCV_H HlyD_2 HlyD_3 HlyD_D23 HlyD_D4 HMBD LAL_C2 NAPRTase_N NQRA OEP Peptidase_M23 PGM1_C PTS_EIIA_1 PurK_C PYNP_C QRPTase_N RnfC_N


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Curation and family details

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Seed source: Pfam-B_1294 (release 3.0)
Previous IDs: Apocytochrome_F;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A
Number in seed: 51
Number in full: 423
Average length of the domain: 111.00 aa
Average identity of full alignment: 62 %
Average coverage of the sequence by the domain: 34.65 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 30.4 30.4
Trusted cut-off 30.4 30.6
Noise cut-off 30.3 30.3
Model length: 118
Family (HMM) version: 22
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Species distribution

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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Apocytochr_F_C domain has been found. There are 38 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0R0K4N7 View 3D Structure Click here
P0C389 View 3D Structure Click here
P46617 View 3D Structure Click here
P49161 View 3D Structure Click here
P56771 View 3D Structure Click here