5O4C: PDB entry 5O4C

Name: PDB 5O4C: From macrocrystals to microcrystals: a strategy for membrane protein serial crystallography
Published: 2017-08-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: membrane protein

From macrocrystals to microcrystals: a strategy for membrane protein serial crystallography. Determined by X-ray diffraction at 2.8 Å resolution. Released 16 Aug 2017.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Blastochloris viridis
Chains: 4
Atoms: 10,196
Mol. weight: 144.54 kDa
Ligands: HTO, LDA, DGA, HEC
Released: 16 Aug 2017

Explore 5O4C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5O4C contains 84 α-helices and 54 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain C: 26 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	1
β-strand	22-23	2	1
α-helix	25-36	12
α-helix	39-44	6
β-strand	51	1	2
α-helix	52-55	4
β-strand	66	1	2
α-helix	67-81	15
α-helix	87-89	3
β-strand	92	1	3
β-strand	95	1	3
α-helix	102-120	19
α-helix	122-125	4
α-helix	132-136	5
β-strand	144	1	4
β-strand	146	1	5
β-strand	155	1	4
α-helix	159-161	3
α-helix	169-171	3
α-helix	172-177	6
α-helix	189	1
α-helix	190-194	5
α-helix	210	1
β-strand	211	1	6
α-helix	217-219	3
α-helix	221-222	2
α-helix	224-240	17
α-helix	244-246	3
β-strand	248	1	7
α-helix	250-252	3
β-strand	257	1	8
β-strand	260	1	7
α-helix	262-277	16
α-helix	278-282	5
α-helix	283-286	4
α-helix	299-301	3
β-strand	302	1	5
α-helix	305-309	5
α-helix	315-318	4
α-helix	326-328	3

Chain H: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	6
β-strand	5	1	9
β-strand	11	1	9
α-helix	12-25	14
α-helix	26-32	7
α-helix	33-35	3
β-strand	44	1	10
α-helix	56-60	5
α-helix	63-65	3
β-strand	66-69	4	11
β-strand	75-78	4	11
α-helix	87-88	2
β-strand	90-92	3	12
α-helix	99-100	2
β-strand	101-103	3	12
α-helix	107-110	4
α-helix	113-115	3
β-strand	124	1	13
β-strand	126	1	14
β-strand	132	1	14
β-strand	134-136	3	15
β-strand	144-145	2	16
β-strand	156-158	3	15
β-strand	164-174	11	15
β-strand	179-187	9	15
β-strand	192-197	6	15
α-helix	198-200	3
β-strand	202-203	2	15
β-strand	208-209	2	15
α-helix	216-220	5
β-strand	231	1	13
α-helix	232-248	17
α-helix	251-253	3

Chain L: 19 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	10
α-helix	7-9	3
β-strand	11	1	12
α-helix	19-21	3
β-strand	25-26	2	17
β-strand	29-30	2	17
α-helix	32-54	23
β-strand	66	1	18
α-helix	71-73	3
α-helix	80-82	3
α-helix	84-111	28
α-helix	116-129	14
α-helix	130-134	5
α-helix	135-139	5
α-helix	142-144	3
β-strand	148	1	18
α-helix	152-163	12
α-helix	167-169	3
α-helix	171-198	28
α-helix	204-206	3
α-helix	209-220	12
β-strand	222	1	19
α-helix	226-250	25
β-strand	251	1	20
β-strand	255	1	20
α-helix	259-262	4
α-helix	264-267	4
α-helix	270-272	3

Chain M: 26 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	11	1	15
β-strand	12-13	2	16
α-helix	15-17	3
α-helix	19-21	3
α-helix	25-27	3
β-strand	28-29	2	21
β-strand	33-34	2	19
α-helix	38-40	3
β-strand	45-46	2	19
β-strand	49-50	2	21
α-helix	53-75	23
α-helix	81-87	7
α-helix	88-90	3
β-strand	93	1	22
α-helix	104-106	3
α-helix	107-109	3
α-helix	111-137	27
α-helix	143-156	14
α-helix	157-161	5
α-helix	162-166	5
α-helix	169-171	3
α-helix	173-174	2
β-strand	175	1	22
α-helix	177-190	14
α-helix	194-196	3
α-helix	198-223	26
α-helix	225-227	3
α-helix	232-237	6
α-helix	241-254	14
α-helix	260-284	25
β-strand	285	1	23
β-strand	289	1	23
α-helix	292-298	7
α-helix	310-311	2
β-strand	312	1	8
α-helix	315-317	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Photosynthetic reaction center cytochrome c subunit	C	protein	336	Blastochloris viridis	P07173 (AlphaFold model)
Reaction center protein H chain	H	protein	258	Blastochloris viridis	P06008 (AlphaFold model)
Reaction center protein L chain	L	protein	273	Blastochloris viridis	P06009 (AlphaFold model)
Reaction center protein M chain	M	protein	323	Blastochloris viridis	P06010 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>5O4C_1 Photosynthetic reaction center cytochrome c subunit (chains C)
CFEPPPATTTQTGFRGLSMGEVLHPATVKAKKERDAQYPPALAAVKAEGPPVSQVYKNVK
VLGNLTEAEFLRTMTAITEWVSPQEGCTYCHDENNLASEAKYPYVVARRMLEMTRAINTN
WTQHVAQTGVTCYTCHRGTPLPPYVRYLEPTLPLNNRETPTHVERVETRSGYVVRLAKYT
AYSALNYDPFTMFLANDKRQVRVVPQTALPLVGVSRGKERRPLSDAYATFALMMSISDSL
GTNCTFCHNAQTFESWGKKSTPQRAIAWWGIRMVRDLNMNYLAPLNASLPASRLGRQGEA
PQADCRTCHQGVTKPLFGASRLKDYPELGPIKAAAK

Sequence of entity 2 (H), FASTA

>5O4C_2 Reaction center protein H chain (chains H)
MYHGALAQHLDIAQLVWYAQWLVIWTVVLLYLRREDRREGYPLVEPLGLVKLAPEDGQVY
ELPYPKTFVLPHGGTVTVPRRRPETRELKLAQTDGFEGAPLQPTGNPLVDAVGPASYAER
AEVVDATVDGKAKIVPLRVATDFSIAEGDVDPRGLPVVAADGVEAGTVTDLWVDRSEHYF
RYLELSVAGSARTALIPLGFCDVKKDKIVVTSILSEQFANVPRLQSRDQITLREEDKVSA
YYAGGLLYATPERAESLL

Sequence of entity 3 (L), FASTA

>5O4C_3 Reaction center protein L chain (chains L)
ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWD
PFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLA
FCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFL
FVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNI
FLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS

Sequence of entity 4 (M), FASTA

>5O4C_4 Reaction center protein M chain (chains M)
ADYQTIYTQIQARGPHITVSGEWGDNDRVGKPFYSYWLGKIGDAQIGPIYLGASGIAAFA
FGSTAILIILFNMAAEVHFDPLQFFRQFFWLGLYPPKAQYGMGIPPLHDGGWWLMAGLFM
TLSLGSWWIRVYSRARALGLGTHIAWNFAAAIFFVLCIGCIHPTLVGSWSEGVPFGIWPH
IDWLTAFSIRYGNFYYCPWHGFSIGFAYGCGLLFAAHGATILAVARFGGDREIEQITDRG
TAVERAALFWRWTIGFNATIESVHRWGWFFSLMVMVSASVGILLTGTFVDNWYLWCVKHG
AAPDYPAYLPATPDPASLPGAPK

Ligands and cofactors

ID	Name	Formula	Copies
HTO	Heptane-1,2,3-triol	C7 H16 O3	2
LDA	Lauryl dimethylamine-N-oxide	C14 H31 N O	4
DGA	Diacyl glycerol	C39 H76 O5	1
HEC	Heme C	C34 H36 Fe N4 O4	4
NS5	15-cis-1,2-dihydroneurosporene	C40 H60	1
MQ7	Menaquinone-7	C46 H64 O2	1
FE2	FE (II) ion	Fe	1
BPB	Bacteriopheophytin B	C55 H74 N4 O6	2
BCB	Bacteriochlorophyll B	C55 H72 Mg N4 O6	4

Water and common crystallization additives (SO4) are not listed.

Primary citation

From Macrocrystals to Microcrystals: A Strategy for Membrane Protein Serial Crystallography. Dods, R., Bath, P., Arnlund, D. et al. Structure (2017) 25:1461-1468.e2. DOI 10.1016/j.str.2017.07.002 · PubMed

Other PDB entries of the same protein (UniProt P07173 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2WJN 1.86 Å, Lipidic sponge phase crystal structure of photosynthetic reaction centre from…
3T6E 1.92 Å, Crystal Structure of the Reaction Centre from Blastochloris viridis strain DSM 133 (ATCC…
2WJM 1.95 Å, Lipidic sponge phase crystal structure of the photosynthetic reaction centre from…
3T6D 1.95 Å, Crystal Structure of the Reaction Centre from Blastochloris viridis strain DSM 133 (ATCC…
2I5N 1.96 Å, 1.96 A X-ray structure of photosynthetic reaction center from Rhodopseudomonas…
1DXR 2.0 Å, Photosynthetic reaction center from Rhodopseudomonas viridis - His L168 Phe mutant…
1VRN 2.2 Å, Photosynthetic reaction center blastochloris viridis (ATCC)
7Q7Q 2.25 Å, Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic…
1PRC 2.3 Å, Crystallographic refinement at 2.3 Å resolution and refined model of the photosynthetic…
6PRC 2.3 Å, Photosynthetic reaction center from rhodopseudomonas viridis (dg-420314 (triazine)…
5PRC 2.35 Å, Photosynthetic reaction center from rhodopseudomonas viridis (atrazine complex)
2JBL 2.4 Å, Photosynthetic reaction center from blastochloris viridis

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