9b8p

Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1

Method: ELECTRON MICROSCOPY

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

H(+)-transporting two-sector ATPase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 17	V-type proton ATPase subunit B, brain isoform × 3 （P62815） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） SidK × 3 （Q5ZWW6） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D4A133_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–647； UniProt 1–647 Author chain B； PDBConstruct 1–647； UniProt 1–647 Author chain C； PDBConstruct 1–647； UniProt 1–647

V-type proton ATPase subunit B, brain isoform

OrganismNot specified

UniProt P62815

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 17	H(+)-transporting two-sector ATPase × 3 （D4A133） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） SidK × 3 （Q5ZWW6） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATB2_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–511； UniProt 1–511 Author chain E； PDBConstruct 1–511； UniProt 1–511 Author chain F； PDBConstruct 1–511； UniProt 1–511

ATPase H+-transporting V1 subunit D

OrganismNot specified

UniProt Q6P503

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 17	H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） SidK × 3 （Q5ZWW6） ADENOSINE-5'-DIPHOSPHATE × 1	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	3
Chains and sequence ranges	Author chain H； PDBConstruct 1–247； UniProt 1–247

V-type proton ATPase subunit E 1

OrganismNot specified

UniProt Q6PCU2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 17	H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） SidK × 3 （Q5ZWW6） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATE1_RAT
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain I； PDBConstruct 1–226； UniProt 1–226 Author chain J； PDBConstruct 1–226； UniProt 1–226 Author chain K； PDBConstruct 1–226； UniProt 1–226

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	Protein heterocomplex	Heteromer	Protein 17	H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit G × 3 （Q8R2H0） SidK × 3 （Q5ZWW6） ADENOSINE-5'-DIPHOSPHATE × 1	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	5
Chains and sequence ranges	Author chain L； PDBConstruct 1–119； UniProt 1–119

V-type proton ATPase subunit G

OrganismNot specified

UniProt Q8R2H0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 17	H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） SidK × 3 （Q5ZWW6） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8R2H0_RAT
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain M； PDBConstruct 1–118； UniProt 1–118 Author chain N； PDBConstruct 1–118； UniProt 1–118 Author chain O； PDBConstruct 1–118； UniProt 1–118

SidK

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

UniProt Q5ZWW6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 17	H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZWW6_LEGPH
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain Q； PDBConstruct 1–573； UniProt 1–573 Author chain R； PDBConstruct 1–573； UniProt 1–573 Author chain S； PDBConstruct 1–573； UniProt 1–573

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9b8p
Deposition date deposition_date	2024-03-31
Structure title title	Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1
Keywords keywords	Mmebrane, Synaptic, Complex, PROTON TRANSPORT; PROTON TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

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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.

9b8p__assembly_1__model_1

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

Download this curve (.dat)

9b8p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9b8p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	53.85 Å
Rg (electron density)	53.46 Å
Total Rg	53.72 Å
Atom count	39148
Residues	4966
Excluded volume	700640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9b8p__assembly_1__model_1`	heptadecameric （17）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	H(+)-transporting two-sector ATPase
Molecular weight formula_weight	71483.4 kDa
EC 编号 ec_number	7.1.2.2
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	39148

MCFKFKSDRASGSGLGTDSALRARAGKFSTMDFSKLPKIRDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGDMATIQVYEETSGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPRGVNVSALSRDIKWEFIPSKNLRVGSHITGGDIYGIVNENSLIKHKIMLPPRSRGSVTYIAPPGNYDASDVVLELEFEGVKEKLSMVQVWPVRQVRPVTEKLPANHPLLTGQRVLDALFPCVQGGTTAIPGAFGCGKTVISQSLSKYSNSDVIIYVGCGERGNEMSEVLRDFPELTMEVDGKVESIMKRTALVANTSNMPVAAREASIYTGITLSEYFRDMGYHVSMMADSTSRWAEALREISGRLAEMPADSGYPAYLGARLASFYERAGRVKCLGNPEREGSVSIVGAVSPPGGDFSDPVTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYYDKHFTEFVPLRTKAKEILQEEEDLAEIVQLVGKASLAETDKITLEVAKLIKDDFLQQNGYTPYDRFCPFYKTVGMLSNMISFYDMARRAVETTAQSDNKITWSIIREHMGEILYKLSSMKFKDPVKDGEAKIKADYAQLLEDMQNAFRSLED

Entity 2 Entity 2 polymer

Description description	V-type proton ATPase subunit B, brain isoform
Molecular weight formula_weight	56611.6 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

MALRAMRGIVNGAAPELPVPTGGPMAGAREQALAVSRNYLSQPRLTYKTVSGVNGPLVILDHVKFPRYAEIVHLTLPDGTKRSGQVLEVSGSKAVVQVFEGTSGIDAKKTSCEFTGDILRTPVSEDMLGRVFNGSGKPIDRGPVVLAEDFLDIMGQPINPQCRIYPEEMIQTGISAIDGMNSIARGQKIPIFSAAGLPHNEIAAQICRQAGLVKKSKDVVDYSEENFAIVFAAMGVNMETARFFKSDFEENGSMDNVCLFLNLANDPTIERIITPRLALTTAEFLAYQCEKHVLVILTDMSSYAEALREVSAAREEVPGRRGFPGYMYTDLATIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIYVDRQLHNRQIYPPINVLPSLSRLMKSAIGEGMTRKDHADVSNQLYACYAIGKDVQAMKAVVGEEALTSDDLLYLEFLQKFEKNFITQGPYENRTVYETLDIGWQLLRIFPKEMLKRIPQSTLSEFYPRDSAKH

Entity 3 Entity 3 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

MSGKDRIEIFPSRMAQTIMKARLKGAQTGRNLLKKKSDALTLRFRQILKKIIETKMLMGEVMREAAFSLAEAKFTAGDFSTTVIQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTDSYELTGLARGGEQLAKLKRNYAKAVELLVELASLQTSFVTLDEAIKITNRRVNAIEHVIIPRIERTLAYIITELDEREREEFYRLKKIQEKKKIIKEKSEKDLERRRAAGEVMEPANLLAEEKDEDLLFE

Entity 4 Entity 4 polymer

Description description	V-type proton ATPase subunit E 1
Molecular weight formula_weight	26167.5 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K

MALSDADVQKQIKHMMAFIEQEANEKAEEIDAKAEEEFNIEKGRLVQTQRLKIMEYYEKKEKQIEQQKKIQMSNLMNQARLKVLRARDDLITDLLNEAKQRLSKVVKDTTRYQVLLDGLVLQGLYQLLEPRMIVRCRKQDFPLVKAAVQKAIPMYKIATKKDVDVQIDLEAYLPEDIAGGVEIYNGDRKIKVSNTLESRLDLIAQQMMPEVRGALFGANANRKFLD

Entity 5 Entity 5 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 6 Entity 6 polymer

Description description	V-type proton ATPase subunit G
Molecular weight formula_weight	13690.5 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,O

MASQSQGIQQLLQAEKRAAEKVADARKRKARRLKQAKEEAQMEVEQYRREREQEFQSKQQAAMGSQGNLSAEVEQATRRQVQGMQSSQQRNRERVLTQLLGMVCDVRPQVHPNYRITV

Entity 7 Entity 7 polymer

Description description	SidK
Molecular weight formula_weight	65505.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q,R,S

MSFIKVGIKMGGLTSEQYHSQVVGKIGYIARCMQTIDPENNLKKIREDYQDVLIWAEKNYRFEEILEASKSGKCPNDLDALSRRSLILQELLRLVSSISPFKMKLDLIESQYEKMKQHVNLWKSDYHVKLNQLNQLTDYLKNAAPTPKNNFLRAMTSVLQMQIAQYGITEDNEGINQLFKLGLHLLAMANEKIDEQYHLFKGYVKDQPEESPFEGILPAEDQKILVKTMIDYAMPKLSSKVLQDKLSALSSSDVLTKTLLDSIDRIVKENEKLNALSKVKLGKFGLDIREIEVIYSQALKISPQDALQYTAQQCDAQLLSMAFPDSQNYIIESISNKKVKTIAELIHSKEFIYQIIKTEVFKQVDPNEKIRLQAATELYQLLGRIMDKQINLFTKMNLEQINEYIQTKTKAILDKIPERVELLTFMGFEIPTFKGIETLMTDISHSQDNETLAIAQEFYTNIKNAKNQLLGDKLIEDITPQDVEKFFNQCSQYGSEAAEKLADNRPVLTKIADILTAIARWAISLIGFNTPPQFLAPTRTCVDQVSDEITKIKLKLEDTLGSLQKVQEESLSL

Source Source

Source organism organism	Legionella pneumophila subsp. pneumophila str. Philadelphia 1
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

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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, V1

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

H(+)-transporting two-sector ATPase

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 B, brain isoform

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 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 E 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

V-type proton ATPase subunit F

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 G

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SidK

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9b8p__assembly_1__model_1

9b8p__assembly_1__model_1 | I(q)

9b8p__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer