3d38 Summary

pdbe.org/3d38
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Crystal structure of new trigonal form of photosynthetic reaction center from Blastochloris viridis. Crystals grown in microfluidics by detergent capture.

The structure was published by Li, L., Nachtergaele, S., Seddon, A.M., Tereshko, V., Ponomarenko, N., and Ismagilov, R.F., in 2008 in a paper entitled "Simple host-guest chemistry to modulate the process of concentration and crystallization of membrane proteins by detergent capture in a microfluidic device." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 3.21 Å and deposited in 2008.

The experimental data on which the structure is based was also deposited.

This entry contains 45 copies of 4 unique biopolymers (complete list).

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule most likely forms heterotetramers.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
C Photosynthetic reaction center cytochrome c subunit P07173 (21-356) (CYCR_BLAVI)search Blastochloris viridissearch 99% 336 98%
H Reaction center protein H chain P06008 (1-258) (RCEH_BLAVI)search Blastochloris viridissearch 100% 258 96%
L Reaction center protein L chain P06009 (2-274) (RCEL_BLAVI)search Blastochloris viridissearch 100% 273 100%
M Reaction center protein M chain P06010 (2-324) (RCEM_BLAVI)search Blastochloris viridissearch 100% 323 100%


This entry contains 4 unique UniProt proteins:

UniProt accession Name Organism PDB
P07173 (21 - 356) Photosynthetic reaction center cytochrome c subunit Blastochloris viridis
P06008 (1 - 258) Reaction center protein H chain Blastochloris viridis
P06009 (2 - 274) Reaction center protein L chain Blastochloris viridis
P06010 (2 - 324) Reaction center protein M chain Blastochloris viridis

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
C (P07173) Photosynthetic reaction centre (cytochrome subunit)search Photosynthetic Reaction Center, subunit C, domain 2search PF02276: Photosynthetic reaction centre cytochrome C subunitsearch
H (P06008) Photosynthetic reaction centre, H-chain, cytoplasmic domainsearch, Photosystem II reaction centre subunit H, transmembrane regionsearch Photosynthetic Reaction Center, subunit H, domain 1search, Photosynthetic Reaction Center, subunit H, domain 2search PF03967: Photosynthetic reaction centre, H-chain N-terminal regionsearch, PF05239: PRC-barrel domainsearch
L (P06009) Bacterial photosystem II reaction centre, L and M subunitssearch Membrane spanning alpha-helix pairssearch PF00124: Photosynthetic reaction centre proteinsearch
M (P06010) Bacterial photosystem II reaction centre, L and M subunitssearch Membrane spanning alpha-helix pairssearch PF00124: Photosynthetic reaction centre proteinsearch

Chain ID Molecular function (GO) Cellular component (GO) Biological process (GO)
C (P07173) heme bindingsearch iron ion bindingsearch electron carrier activitysearch metal ion bindingsearch plasma membrane light-harvesting complexsearch membranesearch plasma membranesearch photosynthesis, light reactionsearch oxidation-reduction processsearch photosynthesissearch
H (P06008) electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activitysearch bacteriochlorophyll bindingsearch chlorophyll bindingsearch plasma membrane light-harvesting complexsearch membranesearch plasma membrane-derived chromatophore membranesearch integral to membranesearch photosynthesis, light reactionsearch oxidation-reduction processsearch photosynthesissearch protein-chromophore linkagesearch
L (P06009) electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activitysearch metal ion bindingsearch bacteriochlorophyll bindingsearch chlorophyll bindingsearch plasma membrane light-harvesting complexsearch plasma membrane-derived chromatophore membranesearch membranesearch integral to membranesearch photosynthesis, light reactionsearch protein-chromophore linkagesearch photosynthesissearch oxidation-reduction processsearch photosynthetic electron transport in photosystem IIsearch
M (P06010) electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activitysearch bacteriochlorophyll bindingsearch metal ion bindingsearch chlorophyll bindingsearch plasma membrane light-harvesting complexsearch plasma membrane-derived chromatophore membranesearch integral to membranesearch membranesearch photosynthesis, light reactionsearch photosynthetic electron transport in photosystem IIsearch oxidation-reduction processsearch protein-chromophore linkagesearch photosynthesissearch

Chain InterPro annotation
C Photosynthetic reaction centre, cytochrome c subunitsearch Multihaem cytochromesearch Multihaem cytochrome, photosynthetic reaction centre cytochrome subunit-likesearch
H Photosynthetic reaction centre, H subunitsearch PRC-barrel-likesearch Bacterial photosynthetic reaction centre, H-chain, C-terminalsearch Photosynthetic reaction centre, H subunit, N-terminalsearch PRC-barrel domainsearch
L Photosynthetic reaction centre, L/Msearch Photosynthetic reaction centre, L subunitsearch
M Photosynthetic reaction centre, L/Msearch Photosynthetic reaction centre, M subunitsearch