6RQF

3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Spinacia oleracea with natively bound thylakoid lipids and plastoquinone molecules

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0009055	molecular_function	electron transfer activity
A	0009507	cellular_component	chloroplast
A	0009535	cellular_component	chloroplast thylakoid membrane
A	0009579	cellular_component	thylakoid
A	0015979	biological_process	photosynthesis
A	0016020	cellular_component	membrane
A	0016491	molecular_function	oxidoreductase activity
A	0022904	biological_process	respiratory electron transport chain
A	0045158	molecular_function	electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity
A	0046872	molecular_function	metal ion binding
B	0005750	cellular_component	mitochondrial respiratory chain complex III
B	0006122	biological_process	mitochondrial electron transport, ubiquinol to cytochrome c
B	0008121	molecular_function	ubiquinol-cytochrome-c reductase activity
B	0009055	molecular_function	electron transfer activity
B	0009507	cellular_component	chloroplast
B	0009535	cellular_component	chloroplast thylakoid membrane
B	0009579	cellular_component	thylakoid
B	0009767	biological_process	photosynthetic electron transport chain
B	0015979	biological_process	photosynthesis
B	0016020	cellular_component	membrane
B	0016491	molecular_function	oxidoreductase activity
B	0042651	cellular_component	thylakoid membrane
B	0043229	cellular_component	intracellular organelle
B	0045156	molecular_function	electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
B	0045158	molecular_function	electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity
B	1902600	biological_process	proton transmembrane transport
C	0005506	molecular_function	iron ion binding
C	0009055	molecular_function	electron transfer activity
C	0009507	cellular_component	chloroplast
C	0009535	cellular_component	chloroplast thylakoid membrane
C	0009579	cellular_component	thylakoid
C	0015979	biological_process	photosynthesis
C	0016020	cellular_component	membrane
C	0020037	molecular_function	heme binding
C	0042651	cellular_component	thylakoid membrane
C	0043229	cellular_component	intracellular organelle
C	0046872	molecular_function	metal ion binding
D	0016020	cellular_component	membrane
D	0045158	molecular_function	electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity
D	0051537	molecular_function	2 iron, 2 sulfur cluster binding
E	0009055	molecular_function	electron transfer activity
E	0009507	cellular_component	chloroplast
E	0009512	cellular_component	cytochrome b6f complex
E	0009535	cellular_component	chloroplast thylakoid membrane
E	0009579	cellular_component	thylakoid
E	0015979	biological_process	photosynthesis
E	0016020	cellular_component	membrane
E	0045158	molecular_function	electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity
F	0009507	cellular_component	chloroplast
F	0009512	cellular_component	cytochrome b6f complex
F	0009535	cellular_component	chloroplast thylakoid membrane
F	0009579	cellular_component	thylakoid
F	0015979	biological_process	photosynthesis
F	0016020	cellular_component	membrane
G	0009507	cellular_component	chloroplast
G	0009512	cellular_component	cytochrome b6f complex
G	0009535	cellular_component	chloroplast thylakoid membrane
G	0009579	cellular_component	thylakoid
G	0015979	biological_process	photosynthesis
G	0016020	cellular_component	membrane
G	0017004	biological_process	cytochrome complex assembly
G	0045158	molecular_function	electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity
H	0009055	molecular_function	electron transfer activity
H	0009507	cellular_component	chloroplast
H	0009512	cellular_component	cytochrome b6f complex
H	0009535	cellular_component	chloroplast thylakoid membrane
H	0009579	cellular_component	thylakoid
H	0015979	biological_process	photosynthesis
H	0016020	cellular_component	membrane
H	0017004	biological_process	cytochrome complex assembly
H	0043229	cellular_component	intracellular organelle
H	0045158	molecular_function	electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity
I	0009055	molecular_function	electron transfer activity
I	0009507	cellular_component	chloroplast
I	0009535	cellular_component	chloroplast thylakoid membrane
I	0009579	cellular_component	thylakoid
I	0015979	biological_process	photosynthesis
I	0016020	cellular_component	membrane
I	0016491	molecular_function	oxidoreductase activity
I	0022904	biological_process	respiratory electron transport chain
I	0045158	molecular_function	electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity
I	0046872	molecular_function	metal ion binding
J	0005750	cellular_component	mitochondrial respiratory chain complex III
J	0006122	biological_process	mitochondrial electron transport, ubiquinol to cytochrome c
J	0008121	molecular_function	ubiquinol-cytochrome-c reductase activity
J	0009055	molecular_function	electron transfer activity
J	0009507	cellular_component	chloroplast
J	0009535	cellular_component	chloroplast thylakoid membrane
J	0009579	cellular_component	thylakoid
J	0009767	biological_process	photosynthetic electron transport chain
J	0015979	biological_process	photosynthesis
J	0016020	cellular_component	membrane
J	0016491	molecular_function	oxidoreductase activity
J	0042651	cellular_component	thylakoid membrane
J	0043229	cellular_component	intracellular organelle
J	0045156	molecular_function	electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
J	0045158	molecular_function	electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity
J	1902600	biological_process	proton transmembrane transport
K	0005506	molecular_function	iron ion binding
K	0009055	molecular_function	electron transfer activity
K	0009507	cellular_component	chloroplast
K	0009535	cellular_component	chloroplast thylakoid membrane
K	0009579	cellular_component	thylakoid
K	0015979	biological_process	photosynthesis
K	0016020	cellular_component	membrane
K	0020037	molecular_function	heme binding
K	0042651	cellular_component	thylakoid membrane
K	0043229	cellular_component	intracellular organelle
K	0046872	molecular_function	metal ion binding
L	0016020	cellular_component	membrane
L	0045158	molecular_function	electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity
L	0051537	molecular_function	2 iron, 2 sulfur cluster binding
M	0009055	molecular_function	electron transfer activity
M	0009507	cellular_component	chloroplast
M	0009512	cellular_component	cytochrome b6f complex
M	0009535	cellular_component	chloroplast thylakoid membrane
M	0009579	cellular_component	thylakoid
M	0015979	biological_process	photosynthesis
M	0016020	cellular_component	membrane
M	0045158	molecular_function	electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity
N	0009507	cellular_component	chloroplast
N	0009512	cellular_component	cytochrome b6f complex
N	0009535	cellular_component	chloroplast thylakoid membrane
N	0009579	cellular_component	thylakoid
N	0015979	biological_process	photosynthesis
N	0016020	cellular_component	membrane
O	0009507	cellular_component	chloroplast
O	0009512	cellular_component	cytochrome b6f complex
O	0009535	cellular_component	chloroplast thylakoid membrane
O	0009579	cellular_component	thylakoid
O	0015979	biological_process	photosynthesis
O	0016020	cellular_component	membrane
O	0017004	biological_process	cytochrome complex assembly
O	0045158	molecular_function	electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity
P	0009055	molecular_function	electron transfer activity
P	0009507	cellular_component	chloroplast
P	0009512	cellular_component	cytochrome b6f complex
P	0009535	cellular_component	chloroplast thylakoid membrane
P	0009579	cellular_component	thylakoid
P	0015979	biological_process	photosynthesis
P	0016020	cellular_component	membrane
P	0017004	biological_process	cytochrome complex assembly
P	0043229	cellular_component	intracellular organelle
P	0045158	molecular_function	electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	14
Details	binding site for residue HEM I 301

Chain	Residue
A	PHE189
I	GLY135
I	LEU138
I	PRO139
I	HIS187
I	PRO192
I	GLN47
I	GLY51
I	MET54
I	VAL69
I	ARG83
I	HIS86
I	ARG87
I	PHE131

---

site_id	AC2
Number of Residues	15
Details	binding site for residue HEM I 302

Chain	Residue
I	TYR34
I	THR40
I	HIS100
I	VAL101
I	ARG103
I	VAL104
I	ARG114
I	THR117
I	TRP118
I	GLY121
I	HIS202
I	PHE203
I	ILE206
I	SER212
I	HEC303

---

site_id	AC3
Number of Residues	6
Details	binding site for residue HEC I 303

Chain	Residue
A	PL9306
I	CYS35
I	ARG207
I	HEM302
J	PHE40
J	VAL43

---

site_id	AC4
Number of Residues	12
Details	binding site for residue CLA I 304

Chain	Residue
A	SQD307
I	MET97
I	PHE102
I	VAL133
I	PL9306
J	TYR80
J	PRO83
J	VAL84
J	GLY136
J	VAL139
J	LMG201
J	PGV202

---

site_id	AC5
Number of Residues	5
Details	binding site for residue BCR I 305

Chain	Residue
I	PHE33
N	THR17
O	LEU35
P	PHE15
P	LEU19

---

site_id	AC6
Number of Residues	9
Details	binding site for residue PL9 I 306

Chain	Residue
A	LEU12
I	LEU116
I	VAL119
I	VAL126
I	MET201
I	LEU204
I	MET205
I	LYS208
I	CLA304

---

site_id	AC7
Number of Residues	4
Details	binding site for residue 6PL I 307

Chain	Residue
A	PRO164
A	PL9305
I	ASN77
K	PGV302

---

site_id	AC8
Number of Residues	11
Details	binding site for residue LMG J 201

Chain	Residue
I	PHE102
I	CLA304
J	TRP79
J	GLY136
J	THR137
J	ILE145
J	THR148
J	LEU149
N	ALA3
N	PHE7
O	LEU11

---

site_id	AC9
Number of Residues	9
Details	binding site for residue PGV J 202

Chain	Residue
I	CLA304
J	SER103
J	GLY107
J	LEU114
J	GLU115
J	ASN118
J	ARG126
J	VAL128
J	ALA129

---

site_id	AD1
Number of Residues	17
Details	binding site for residue HEC K 301

Chain	Residue
K	GLY157
K	ILE159
K	TYR160
K	TYR1
K	PRO2
K	PHE4
K	CYS21
K	CYS24
K	HIS25
K	GLN59
K	ASN70
K	VAL71
K	GLY72
K	VAL74
K	ASN153
K	GLY155
K	ARG156

---

site_id	AD2
Number of Residues	7
Details	binding site for residue PGV K 302

Chain	Residue
I	ASN77
I	LEU81
I	6PL307
K	ASP247
K	LEU249
K	ARG250
L	TYR32

---

site_id	AD3
Number of Residues	7
Details	binding site for residue FES L 201

Chain	Residue
L	CYS107
L	HIS109
L	LEU110
L	CYS112
L	CYS125
L	HIS128
L	GLY129

---

site_id	AD4
Number of Residues	9
Details	binding site for residue SQD L 202

Chain	Residue
J	TRP32
J	PRO41
K	LYS271
K	PHE275
L	ARG15
L	ASN19
L	LEU22
L	LEU23
L	LEU26

---

site_id	AD5
Number of Residues	11
Details	binding site for residue 6PL N 101

Chain	Residue
I	MET96
M	MET1
M	THR3
M	TYR7
N	GLU5
N	ARG8
N	VAL12
N	GLY15
O	PHE5
P	MET12
P	PHE15

---

site_id	AD6
Number of Residues	19
Details	binding site for residue HEM A 301

Chain	Residue
A	PHE44
A	VAL48
A	GLY51
A	MET54
A	VAL69
A	ARG83
A	HIS86
A	ARG87
A	ALA90
A	MET93
A	THR128
A	PHE131
A	GLY135
A	LEU138
A	PRO139
A	HIS187
A	PRO192
B	GLU78
I	PHE189

---

site_id	AD7
Number of Residues	16
Details	binding site for residue HEM A 302

Chain	Residue
A	TYR34
A	GLY38
A	MET97
A	HIS100
A	VAL101
A	ARG103
A	VAL104
A	GLY109
A	THR117
A	GLY121
A	HIS202
A	PHE203
A	ILE206
A	ILE211
A	SER212
A	HEC303

---

site_id	AD8
Number of Residues	11
Details	binding site for residue HEC A 303

Chain	Residue
A	VAL30
A	TYR34
A	CYS35
A	GLY38
A	LEU41
A	PHE203
A	ARG207
A	GLY210
A	ILE211
A	HEM302
B	ASN25

---

site_id	AD9
Number of Residues	8
Details	binding site for residue CLA A 304

Chain	Residue
A	PHE102
A	TYR105
B	TYR80
B	PRO83
B	LEU108
B	PHE133
B	GLY136
F	LMG101

---

site_id	AE1
Number of Residues	3
Details	binding site for residue PL9 A 305

Chain	Residue
A	MET201
A	PL9306
I	6PL307

---

site_id	AE2
Number of Residues	12
Details	binding site for residue PL9 A 306

Chain	Residue
A	VAL48
A	LEU193
A	ALA196
A	PL9305
I	PHE44
I	PHE189
I	PRO192
I	MET199
I	ARG207
I	HEC303
J	LEU36
J	PHE40

---

site_id	AE3
Number of Residues	4
Details	binding site for residue SQD A 307

Chain	Residue
A	PHE56
D	VAL42
I	LEU186
I	CLA304

---

site_id	AE4
Number of Residues	7
Details	binding site for residue PGV A 308

Chain	Residue
A	GLU75
A	ASN77
A	PHE78
A	TRP80
A	LEU81
B	VAL52
D	MET33

---

site_id	AE5
Number of Residues	7
Details	binding site for residue PGV B 201

Chain	Residue
B	SER103
B	GLY107
B	LEU114
B	ASN118
B	ARG126
B	VAL128
B	ALA129

---

site_id	AE6
Number of Residues	15
Details	binding site for residue HEC C 301

Chain	Residue
C	TYR1
C	PHE4
C	CYS21
C	CYS24
C	HIS25
C	GLN59
C	ASN70
C	GLY72
C	PRO117
C	ASN153
C	GLY155
C	ARG156
C	GLY157
C	ILE159
C	TYR160

---

site_id	AE7
Number of Residues	9
Details	binding site for residue SQD C 302

Chain	Residue
B	TRP32
B	PRO33
B	PRO41
C	LYS271
C	PHE275
D	ASN19
D	LEU22
D	LEU23
D	LEU26

---

site_id	AE8
Number of Residues	6
Details	binding site for residue FES D 201

Chain	Residue
D	CYS107
D	HIS109
D	LEU110
D	CYS125
D	HIS128
D	SER130

---

site_id	AE9
Number of Residues	8
Details	binding site for residue 6PL E 101

Chain	Residue
A	MET96
B	ASN51
E	MET1
E	THR3
E	LEU4
E	TYR7
F	MET13
H	TRP8

---

site_id	AF1
Number of Residues	6
Details	binding site for residue LMG F 101

Chain	Residue
A	CLA304
B	THR148
B	LEU149
B	LEU159
F	ASN1
F	PHE7

---

site_id	AF2
Number of Residues	4
Details	binding site for residue BCR H 101

Chain	Residue
A	PHE33
A	ILE39
H	PHE15
H	SER18

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	40
Details	TRANSMEM: Helical => ECO:0000255

Chain	Residue	Details
P	ILE3-VAL23
H	ILE3-VAL23
J	THR131-ILE151
B	LEU36-VAL56
B	LEU95-GLU115
B	THR131-ILE151
A	LEU116-TYR136
A	LEU186-ILE206

---

site_id	SWS_FT_FI2
Number of Residues	44
Details	TRANSMEM: Helical => ECO:0000255

Chain	Residue	Details
N	ILE6-LEU28
F	ILE6-LEU28
L	CYS125
L	HIS128
D	CYS107
D	HIS109
D	CYS125
D	HIS128

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	TOPO_DOM: Stromal => ECO:0000255

Chain	Residue	Details
N	ARG29
F	ARG29
C	CYS21
C	CYS24

---

site_id	SWS_FT_FI4
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269|PubMed:31723268, ECO:0000269|PubMed:36638176, ECO:0007744|PDB:6RQF, ECO:0007744|PDB:7QRM

Chain	Residue	Details
I	ARG83
I	ARG103
I	SER212
A	ARG83
A	ARG103
A	SER212

---

site_id	SWS_FT_FI5
Number of Residues	8
Details	BINDING: axial binding residue => ECO:0000269|PubMed:31723268, ECO:0000269|PubMed:36638176, ECO:0007744|PDB:6RQF, ECO:0007744|PDB:7QRM

Chain	Residue	Details
I	HIS86
I	HIS100
I	HIS187
I	HIS202
A	HIS86
A	HIS100
A	HIS187
A	HIS202

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269|PubMed:36638176, ECO:0007744|PDB:7QRM

Chain	Residue	Details
I	ARG207
A	ARG207

---