9b8o

Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo

Method: ELECTRON MICROSCOPY

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

ATPase H+-transporting V1 subunit D

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 19 其他Polymer 9	V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PHOSPHATIDYLETHANOLAMINE × 9 CHOLESTEROL × 30	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6P503_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain H； PDBConstruct 1–247； UniProt 1–247

V-type proton ATPase subunit S1

OrganismNot specified

UniProt O54715

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 19 其他Polymer 9	ATPase H+-transporting V1 subunit D × 1 （Q6P503） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PHOSPHATIDYLETHANOLAMINE × 9 CHOLESTEROL × 30	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VAS1_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–463； UniProt 1–463

Synaptophysin

OrganismNot specified

UniProt P07825

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 19 其他Polymer 9	ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PHOSPHATIDYLETHANOLAMINE × 9 CHOLESTEROL × 30	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYPH_RAT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain U； PDBConstruct 1–307； UniProt 1–307

V-type proton ATPase 116 kDa subunit a 1

OrganismNot specified

UniProt P25286

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 19 其他Polymer 9	ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PHOSPHATIDYLETHANOLAMINE × 9 CHOLESTEROL × 30	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPP1_RAT
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain a； PDBConstruct 1–826； UniProt 1–826

ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a

OrganismNot specified

UniProt B0K022

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 19 其他Polymer 9	ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PHOSPHATIDYLETHANOLAMINE × 9 CHOLESTEROL × 30	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B0K022_RAT
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain b； PDBConstruct 1–205； UniProt 1–205

V-type proton ATPase subunit

OrganismNot specified

UniProt Q5M7T6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 19 其他Polymer 9	ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PHOSPHATIDYLETHANOLAMINE × 9 CHOLESTEROL × 30	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5M7T6_RAT
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain d； PDBConstruct 1–351； UniProt 1–351

V-type proton ATPase subunit e 2

OrganismNot specified

UniProt Q5EB76

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 19 其他Polymer 9	ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PHOSPHATIDYLETHANOLAMINE × 9 CHOLESTEROL × 30	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VA0E2_RAT
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain e； PDBConstruct 1–81； UniProt 1–81

Rnasek protein

OrganismNot specified

UniProt A0A8J8YMT9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 19 其他Polymer 9	ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PHOSPHATIDYLETHANOLAMINE × 9 CHOLESTEROL × 30	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8J8YMT9_RAT
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain f； PDBConstruct 1–86； UniProt 5–90

V-type proton ATPase 16 kDa proteolipid subunit c

OrganismNot specified

UniProt P63081

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 19 其他Polymer 9	ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） Renin receptor × 1 （Q6AXS4） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PHOSPHATIDYLETHANOLAMINE × 9 CHOLESTEROL × 30	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATL_RAT
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain g； PDBConstruct 1–155； UniProt 1–155 Author chain h； PDBConstruct 1–155； UniProt 1–155 Author chain i； PDBConstruct 1–155； UniProt 1–155 Author chain j； PDBConstruct 1–155； UniProt 1–155 Author chain k； PDBConstruct 1–155； UniProt 1–155 Author chain l； PDBConstruct 1–155； UniProt 1–155 Author chain m； PDBConstruct 1–155； UniProt 1–155 Author chain n； PDBConstruct 1–155； UniProt 1–155 Author chain o； PDBConstruct 1–155； UniProt 1–155

Renin receptor

OrganismNot specified

UniProt Q6AXS4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 19 其他Polymer 9	ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PHOSPHATIDYLETHANOLAMINE × 9 CHOLESTEROL × 30	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RENR_RAT
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain p； PDBConstruct 1–350； UniProt 1–350

V-type proton ATPase subunit F

OrganismNot specified

UniProt P50408

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 19 其他Polymer 9	ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PHOSPHATIDYLETHANOLAMINE × 9 CHOLESTEROL × 30	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATF_RAT
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain L； PDBConstruct 1–119； UniProt 1–119

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9b8o
Deposition date deposition_date	2024-03-31
Structure title title	Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo
Keywords keywords	Membrane, Synaptic, Complex, PROTON TRANSPORT; PROTON TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9b8o__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9b8o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9b8o__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	45.65 Å
Rg (electron density)	44.31 Å
Total Rg	44.38 Å
Atom count	24407
Residues	3028
Excluded volume	452580 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9b8o__assembly_1__model_1`	nonadecameric （19）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (19)

Entity 1 Entity 1 polymer

Description description	ATPase H+-transporting V1 subunit D
Molecular weight formula_weight	28359.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	24407

MSGKDRIEIFPSRMAQTIMKARLKGAQTGRNLLKKKSDALTLRFRQILKKIIETKMLMGEVMREAAFSLAEAKFTAGDFSTTVIQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTDSYELTGLARGGEQLAKLKRNYAKAVELLVELASLQTSFVTLDEAIKITNRRVNAIEHVIIPRIERTLAYIITELDEREREEFYRLKKIQEKKKIIKEKSEKDLERRRAAGEVMEPANLLAEEKDEDLLFE

Entity 2 Entity 2 polymer

Description description	V-type proton ATPase subunit S1
Molecular weight formula_weight	51160.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MMAATVVSRIRTGTRWAPVLWLLLSLVAVAAAVAAEQQVPLVLWSSDRDLWAPVADTHEGHITSDMQLSTYLDPALELGPRNVLLFLQDKLSIEDFTAYGGVFGNKQDSAFSNLENALDLAPSSLVLPAVDWYAISTLTTYLQEKLGASPLHVDLATLKELKLNASLPALLLIRLPYTASSGLMAPREVLTGNDEVIGQVLSTLESEDVPYTAALTAVRPSRVARDVAMVAGGLGRQLLQTQVASPAIHPPVSYNDTAPRILFWAQNFSVAYKDEWKDLTSLTFGVENLNLTGSFWNDSFAMLSLTYEPLFGATVTFKFILASRFYPVSARYWFTMERLEIHSNGSVAHFNVSQVTGPSIYSFHCEYVSSLSKKGSLLVTNVPSLWQMTLHNFQIQAFNVTGEQFSYASDCAGFFSPGIWMGLLTTLFMLFIFTYGLHMILSLKTMDRFDDRKGPTITLTQIV

Entity 3 Entity 3 polymer

Description description	Synaptophysin
Molecular weight formula_weight	33331.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

MDVVNQLVAGGQFRVVKEPLGFVKVLQWVFAIFAFATCGSYTGELRLSVECANKTESALNIEVEFEYPFRLHQVYFDAPSCVKGGTTKIFLVGDYSSSAEFFVTVAVFAFLYSMGALATYIFLQNKYRENNKGPMMDFLATAVFAFMWLVSSSAWAKGLSDVKMATDPENIIKEMPMCRQTGNTCKELRDPVTSGLNTSVVFGFLNLVLWVGNLWFVFKETGWAAPFMRAPPGAPEKQPAPGDAYGDAGYGQGPGGYGPQDSYGPQGGYQPDYGQPASGGGGYGPQGDYGQQGYGQQGAPTSFSNQM

Entity 4 Entity 4 polymer

Description description	V-type proton ATPase 116 kDa subunit a 1
Molecular weight formula_weight	94950.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a

MGELFRSEEMTLAQLFLQSEAAYCCVSELEELGKVQFRDLNPDVNVFQRKFVNEVRRCEEMDRKLRFVEKEIRKANIPIMDTGENPEVPFPRDMIDLEANFEKIENELKEINTNQEALKRNFLELTELKFILRKTQQFFDEMADPDLLEESSSLLEPNEMGRGAPLRLGFVAGVINRERIPTFERMLWRVCRGNVFLRQAEIENPLEDPVTGDYVHKSVFIIFFQGDQLKNRVKKICEGFRASLYPCPETPQERKEMASGVNTRIDDLQMVLNQTEDHRQRVLQAAAKNIRVWFIKVRKMKAIYHTLNLCNIDVTQKCLIAEVWCPVTDLDSIQFALRRGTEHSGSTVPSILNRMQTNQTPPTYNKTNKFTHGFQNIVDAYGIGTYREINPAPYTVITFPFLFAVMFGDFGHGILMTLFAVWMVLRESRILSQKNENEMFSMVFSGRYIILLMGLFSIYTGLIYNDCFSKSLNIFGSSWSVRPMFTIGNWTEETLLGSSVLQLNPAIPGVFGGPYPFGIDPIWNIATNKLTFLNSFKMKMSVILGIIHMLFGVSLSLFNHIYFKKPLNIYFGFIPEIIFMSSLFGYLVILIFYKWTAYDAHSSRNAPSLLIHFINMFLFSYPESGNAMLYSGQKGIQCFLIVVAMLCVPWMLLFKPLILRHQYLRKKHLGTLNFGGIRVGNGPTEEDAEIIQHDQLSTHSEDAEEPTEDEVFDFGDTMVHQAIHTIEYCLGCISNTASYLRLWALSLAHAQLSEVLWTMVIHIGLHVRSLAGGLGLFFIFAAFATLTVAILLIMEGLSAFLHALRLHWVEFQNKFYTGTGFKFLPF

Entity 5 Entity 5 polymer

Description description	ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
Molecular weight formula_weight	21618.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b

MTGLELLYLGIFVAFWACMIVVGICYTIFDLGFRFDVAWFLTETSPFMWSNLGIGLAISLSVVGAAWGIYITGSSIIGGGVKAPRIKTKNLVSIIFCEAVAIYGIIMAIVISNMAEPFSATDPKAIGHRNYHAGYSMFGAGLTVGLSNLFCGVCVGIVGSGAALADAQNPSLFVKILIVEIFGSAIGLFGVIVAILQTSRVKMGD

Entity 6 Entity 6 polymer

Description description	V-type proton ATPase subunit
Molecular weight formula_weight	40341.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	d

MSFFPELYFNVDNGYLEGLVRGLKAGVLSQADYLNLVQCETLEDLKLHLQSTDYGNFLANEASPLTVSVIDDKLKEKMVVEFRHMRNHAYEPLASFLDFITYSYMIDNVILLITGTLHQRSIAELVPKCHPLGSFEQMEAVNIAQTPAELYNAILVDTPLAAFFQDCISEQDLDEMNIEIIRNTLYKAYLESFYKFCTLLGGTTADAMCPILEFEADRRAFIITINSFGTELSKEDRAKLFPHCGRLYPEGLAQLARADDYEQVKNVADYYPEYKLLFEGAGSNPGDKTLEDRFFEHEVKLNKLAFLNQFHFGVFYAFVKLKEQECRNIVWIAECIAQRHRAKIDNYIPIF

Entity 7 Entity 7 polymer

Description description	V-type proton ATPase subunit e 2
Molecular weight formula_weight	9203.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	e

MTAHSFALPVIIFTTFWGLIGIAGPWFVPKGPNRGVIITMLVATAVCCYLFWLIAILAQLNPLFGPQLKNETIWYVRFLWE

Entity 8 Entity 8 polymer

Description description	Rnasek protein
Molecular weight formula_weight	9502.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	f

LCCGPKLAACGIVLSAWGVIMLIMLGIFFNVHSAVLIEDVPFTEKDFENGPQNIYNLYEQVSYNCFIAAGLYLLLGGFSFCQVRLN

Entity 9 Entity 9 polymer

Description description	V-type proton ATPase 16 kDa proteolipid subunit c
Molecular weight formula_weight	15815.8 kDa
Source method src_method	nat
Copy count entity_count	9

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	g,h,i,j,k,l,m,n,o

MADIKNNPEYSSFFGVMGASSAMVFSAMGAAYGTAKSGTGIAAMSVMRPELIMKSIIPVVMAGIIAIYGLVVAVLIANSLTDGITLYRSFLQLGAGLSVGLSGLAAGFAIGIVGDAGVRGTAQQPRLFVGMILILIFAEVLGLYGLIVALILSTK

Entity 10 Entity 10 polymer

Description description	Renin receptor
Molecular weight formula_weight	39118.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	p

MAVLVVLLSSLVSSALANEFSILRSPGSVVFRNGNWPIPGDRIPDVAALSMGFSVKEDLSWPGLAVGNLFHRPRATIMVTVKGVDKLALPTGSVISYPLENAVPFSLDSVANSIHSLFSEETPVVLQLAPSEERVYMVGKANSVFEDLSVTLRQLRNRLFQENSVLNSLPLNSLSRNNEVDLLFLSELQVLHDISSLLSRHKHLAKDHSPDLYSLELAGLDELGKRYGEDSEQFRDASRILVDALQKFADDMYSLYGGNAVVELVTVKSFDTSLVRKSRTILETKQENTQSPYNLAYKYNLEYSVVFNLVLWIMTGLALAVIITSYNIWNMDPGYDSIIYRMTNQKIRMD

Entity 11 Entity 11 polymer

Description description	V-type proton ATPase subunit F
Molecular weight formula_weight	13389.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MAGRGKLIAVIGDEDTVTGFLLGGIGELNKNRHPNFLVVEKDTTINEIEDTFRQFLNRDDIGIILINQYIAEMVRHALDAHQRSIPAVLEIPSKEHPYDAAKDSILRRAKGMFTAEDLR

Entity 12 Entity 12 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	8

Entity 13 Entity 13 branched

Description description	;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1883.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 14 Entity 14 non-polymer

Description description	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	790.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 15 Entity 15 non-polymer

Description description	methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate
Molecular weight formula_weight	534.6 kDa
Source method src_method	man
Copy count entity_count	1

Entity 16 Entity 16 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 17 Entity 17 non-polymer

Description description	(7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE
Molecular weight formula_weight	524.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 18 Entity 18 non-polymer

Description description	PHOSPHATIDYLETHANOLAMINE
Molecular weight formula_weight	734.0 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 19 Entity 19 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	30

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	3.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	198533

Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo

1. Protein Identity and Related Structures Protein Identity & Related Structures

ATPase H+-transporting V1 subunit D

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type proton ATPase subunit S1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Synaptophysin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type proton ATPase 116 kDa subunit a 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type proton ATPase subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type proton ATPase subunit e 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Rnasek protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type proton ATPase 16 kDa proteolipid subunit c

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Renin receptor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer