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- PDB-7unf: CryoEM structure of a mEAK7 bound human V-ATPase complex -

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Basic information

Entry
Database: PDB / ID: 7unf
TitleCryoEM structure of a mEAK7 bound human V-ATPase complex
Components
  • (V-type proton ATPase ...) x 14
  • ATPase H(+)-transporting lysosomal accessory protein 2
  • KIAA1609 protein, isoform CRA_a
  • Ribonuclease kappa
KeywordsPROTON TRANSPORT / mTOR signaling
Function / homology
Function and homology information


Blockage of phagosome acidification / proton-transporting two-sector ATPase complex / Ion channel transport / plasma membrane proton-transporting V-type ATPase complex / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / renal tubular secretion / Nef Mediated CD8 Down-regulation / ATPase-coupled ion transmembrane transporter activity / Golgi lumen acidification ...Blockage of phagosome acidification / proton-transporting two-sector ATPase complex / Ion channel transport / plasma membrane proton-transporting V-type ATPase complex / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / renal tubular secretion / Nef Mediated CD8 Down-regulation / ATPase-coupled ion transmembrane transporter activity / Golgi lumen acidification / synaptic vesicle lumen acidification / vacuolar transport / proton-transporting V-type ATPase, V0 domain / extrinsic component of synaptic vesicle membrane / Transferrin endocytosis and recycling / cellular response to increased oxygen levels / vacuolar proton-transporting V-type ATPase, V1 domain / endosome to plasma membrane protein transport / vacuolar proton-transporting V-type ATPase, V0 domain / clathrin-coated vesicle membrane / lysosomal lumen acidification / endosomal lumen acidification / regulation of pH / XBP1(S) activates chaperone genes / proton-transporting V-type ATPase complex / Amino acids regulate mTORC1 / protein localization to cilium / vacuolar proton-transporting V-type ATPase complex / osteoclast development / Nef Mediated CD4 Down-regulation / ROS and RNS production in phagocytes / vacuolar acidification / regulation of cellular pH / dendritic spine membrane / azurophil granule membrane / microvillus / proton transmembrane transporter activity / ATPase activator activity / autophagosome membrane / tertiary granule membrane / ficolin-1-rich granule membrane / proton-transporting ATPase activity, rotational mechanism / cilium assembly / RHOA GTPase cycle / regulation of macroautophagy / positive regulation of Wnt signaling pathway / transporter activator activity / H+-transporting two-sector ATPase / specific granule membrane / ATP metabolic process / Insulin receptor recycling / enzyme regulator activity / ruffle / receptor-mediated endocytosis of virus by host cell / proton-transporting ATP synthase activity, rotational mechanism / axon terminus / endoplasmic reticulum-Golgi intermediate compartment membrane / RNA endonuclease activity / proton transmembrane transport / receptor-mediated endocytosis / ossification / secretory granule / brush border membrane / sensory perception of sound / small GTPase binding / transmembrane transport / phagocytic vesicle membrane / endocytosis / apical part of cell / synaptic vesicle membrane / melanosome / signaling receptor activity / ATPase binding / basolateral plasma membrane / Hydrolases; Acting on ester bonds / intracellular iron ion homeostasis / early endosome / endosome / endosome membrane / cilium / apical plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / Neutrophil degranulation / centrosome / endoplasmic reticulum membrane / protein-containing complex binding / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / TLDc domain / TLDc domain / TLDc domain profile. / domain in TBC and LysM domain containing proteins / ATPase, V0 complex, subunit e1/e2, metazoa / V0 complex accessory subunit Ac45 / V-type proton ATPase subunit S1, luminal domain / V-type proton ATPase subunit S1, luminal domain / Renin receptor-like ...: / TLDc domain / TLDc domain / TLDc domain profile. / domain in TBC and LysM domain containing proteins / ATPase, V0 complex, subunit e1/e2, metazoa / V0 complex accessory subunit Ac45 / V-type proton ATPase subunit S1, luminal domain / V-type proton ATPase subunit S1, luminal domain / Renin receptor-like / : / Renin receptor-like transmembrane spanning segment / Renin receptor N-terminal domain / ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / ATPase, V1 complex, subunit A / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Ribonuclease kappa / : / V-type proton ATPase subunit f-like / Vacuolar (H+)-ATPase G subunit / V-type proton ATPase subunit S1/VOA1, transmembrane domain / Vacuolar (H+)-ATPase G subunit / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / V-ATPase proteolipid subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-POV / Renin receptor / KIAA1609 protein, isoform CRA_a / V-type proton ATPase subunit e 1 / V-type proton ATPase subunit G 1 / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase subunit C 1 / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit E 1 ...ADENOSINE-5'-DIPHOSPHATE / Chem-POV / Renin receptor / KIAA1609 protein, isoform CRA_a / V-type proton ATPase subunit e 1 / V-type proton ATPase subunit G 1 / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase subunit C 1 / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit E 1 / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit d 1 / V-type proton ATPase subunit S1 / V-type proton ATPase subunit F / Ribonuclease kappa / V-type proton ATPase 21 kDa proteolipid subunit c'' / V-type proton ATPase 116 kDa subunit a 4 / V-type proton ATPase subunit H / V-type proton ATPase subunit D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.08 Å
AuthorsWang, R. / Li, X.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM135343 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01 HL020948 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL072304 United States
CitationJournal: Nat Commun / Year: 2022
Title: Molecular basis of mEAK7-mediated human V-ATPase regulation.
Authors: Rong Wang / Yu Qin / Xiao-Song Xie / Xiaochun Li /
Abstract: The activity of V-ATPase is well-known to be regulated by reversible dissociation of its V and V domains in response to growth factor stimulation, nutrient sensing, and cellular differentiation. The ...The activity of V-ATPase is well-known to be regulated by reversible dissociation of its V and V domains in response to growth factor stimulation, nutrient sensing, and cellular differentiation. The molecular basis of its regulation by an endogenous modulator without affecting V-ATPase assembly remains unclear. Here, we discover that a lysosome-anchored protein termed (mammalian Enhancer-of-Akt-1-7 (mEAK7)) binds to intact V-ATPase. We determine cryo-EM structure of human mEAK7 in complex with human V-ATPase in native lipid-containing nanodiscs. The structure reveals that the TLDc domain of mEAK7 engages with subunits A, B, and E, while its C-terminal domain binds to subunit D, presumably blocking V-V torque transmission. Our functional studies suggest that mEAK7, which may act as a V-ATPase inhibitor, does not affect the activity of V-ATPase in vitro. However, overexpression of mEAK7 in HCT116 cells that stably express subunit a4 of V-ATPase represses the phosphorylation of ribosomal protein S6. Thus, this finding suggests that mEAK7 potentially links mTOR signaling with V-ATPase activity.
History
DepositionApr 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: V-type proton ATPase 116 kDa subunit a 4
U: KIAA1609 protein, isoform CRA_a
L: V-type proton ATPase catalytic subunit A
M: V-type proton ATPase catalytic subunit A
N: V-type proton ATPase catalytic subunit A
O: V-type proton ATPase subunit B, brain isoform
P: V-type proton ATPase subunit B, brain isoform
Q: V-type proton ATPase subunit B, brain isoform
D: V-type proton ATPase subunit D
b: V-type proton ATPase subunit E 1
c: V-type proton ATPase subunit E 1
d: V-type proton ATPase subunit E 1
e: V-type proton ATPase subunit G 1
f: V-type proton ATPase subunit G 1
g: V-type proton ATPase subunit G 1
F: V-type proton ATPase subunit F
C: V-type proton ATPase subunit C 1
H: V-type proton ATPase subunit H
k: V-type proton ATPase subunit d 1
m: V-type proton ATPase subunit e 1
n: Ribonuclease kappa
s: V-type proton ATPase subunit S1
r: ATPase H(+)-transporting lysosomal accessory protein 2
8: V-type proton ATPase 16 kDa proteolipid subunit
9: V-type proton ATPase 16 kDa proteolipid subunit
1: V-type proton ATPase 21 kDa proteolipid subunit
2: V-type proton ATPase 16 kDa proteolipid subunit
3: V-type proton ATPase 16 kDa proteolipid subunit
4: V-type proton ATPase 16 kDa proteolipid subunit
5: V-type proton ATPase 16 kDa proteolipid subunit
6: V-type proton ATPase 16 kDa proteolipid subunit
7: V-type proton ATPase 16 kDa proteolipid subunit
0: V-type proton ATPase 16 kDa proteolipid subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,115,11551
Polymers1,104,78133
Non-polymers10,33518
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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V-type proton ATPase ... , 14 types, 30 molecules aLMNOPQDbcdefgFCHkms8923456701

#1: Protein V-type proton ATPase 116 kDa subunit a 4 / V-ATPase 116 kDa isoform a 4 / Vacuolar proton translocating ATPase 116 kDa subunit a isoform 4 / ...V-ATPase 116 kDa isoform a 4 / Vacuolar proton translocating ATPase 116 kDa subunit a isoform 4 / Vacuolar proton translocating ATPase 116 kDa subunit a kidney isoform


Mass: 98530.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP6V0A4, ATP6N1B, ATP6N2 / Production host: Homo sapiens (human) / References: UniProt: Q9HBG4
#3: Protein V-type proton ATPase catalytic subunit A / V-ATPase subunit A / V-ATPase 69 kDa subunit / Vacuolar ATPase isoform VA68 / Vacuolar proton pump ...V-ATPase subunit A / V-ATPase 69 kDa subunit / Vacuolar ATPase isoform VA68 / Vacuolar proton pump subunit alpha


Mass: 68379.875 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P38606, H+-transporting two-sector ATPase
#4: Protein V-type proton ATPase subunit B, brain isoform / V-ATPase subunit B 2 / Endomembrane proton pump 58 kDa subunit / HO57 / Vacuolar proton pump subunit B 2


Mass: 56561.500 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P21281
#5: Protein V-type proton ATPase subunit D / V-ATPase subunit D / V-ATPase 28 kDa accessory protein / Vacuolar proton pump subunit D


Mass: 28311.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y5K8
#6: Protein V-type proton ATPase subunit E 1 / V-ATPase subunit E 1 / V-ATPase 31 kDa subunit / p31 / Vacuolar proton pump subunit E 1


Mass: 26183.346 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36543
#7: Protein V-type proton ATPase subunit G 1 / V-ATPase subunit G 1 / V-ATPase 13 kDa subunit 1 / Vacuolar proton pump subunit G 1 / Vacuolar ...V-ATPase subunit G 1 / V-ATPase 13 kDa subunit 1 / Vacuolar proton pump subunit G 1 / Vacuolar proton pump subunit M16


Mass: 13781.547 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75348
#8: Protein V-type proton ATPase subunit F / V-ATPase subunit F / V-ATPase 14 kDa subunit / Vacuolar proton pump subunit F


Mass: 13388.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16864
#9: Protein V-type proton ATPase subunit C 1 / V-ATPase subunit C 1 / Vacuolar proton pump subunit C 1


Mass: 43999.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P21283
#10: Protein V-type proton ATPase subunit H / V-ATPase subunit H / Nef-binding protein 1 / NBP1 / Protein VMA13 homolog / V-ATPase 50/57 kDa ...V-ATPase subunit H / Nef-binding protein 1 / NBP1 / Protein VMA13 homolog / V-ATPase 50/57 kDa subunits / Vacuolar proton pump subunit H / Vacuolar proton pump subunit SFD


Mass: 55949.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UI12
#11: Protein V-type proton ATPase subunit d 1 / V-ATPase subunit d 1 / 32 kDa accessory protein / V-ATPase 40 kDa accessory protein / V-ATPase AC39 ...V-ATPase subunit d 1 / 32 kDa accessory protein / V-ATPase 40 kDa accessory protein / V-ATPase AC39 subunit / p39 / Vacuolar proton pump subunit d 1


Mass: 40369.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61421
#12: Protein V-type proton ATPase subunit e 1 / V-ATPase subunit e 1 / V-ATPase 9.2 kDa membrane accessory protein / V-ATPase M9.2 subunit / ...V-ATPase subunit e 1 / V-ATPase 9.2 kDa membrane accessory protein / V-ATPase M9.2 subunit / Vacuolar proton pump subunit e 1


Mass: 9380.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15342
#14: Protein V-type proton ATPase subunit S1 / V-ATPase subunit S1 / Protein XAP-3 / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / ...V-ATPase subunit S1 / Protein XAP-3 / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / Vacuolar proton pump subunit S1


Mass: 52067.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15904
#16: Protein
V-type proton ATPase 16 kDa proteolipid subunit / V-ATPase 16 kDa proteolipid subunit / Vacuolar proton pump 16 kDa proteolipid subunit


Mass: 15743.655 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27449
#17: Protein V-type proton ATPase 21 kDa proteolipid subunit / V-ATPase 21 kDa proteolipid subunit / Vacuolar proton pump 21 kDa proteolipid subunit / hATPL


Mass: 21418.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99437

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Protein , 3 types, 3 molecules Unr

#2: Protein KIAA1609 protein, isoform CRA_a


Mass: 51096.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: D3DUL8
#13: Protein Ribonuclease kappa / RNase kappa


Mass: 15435.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q6P5S7, Hydrolases; Acting on ester bonds
#15: Protein ATPase H(+)-transporting lysosomal accessory protein 2 / ATPase H(+)-transporting lysosomal-interacting protein 2 / Renin receptor / Renin/prorenin receptor


Mass: 38421.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A1B0GVW0

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Sugars , 3 types, 8 molecules

#18: Polysaccharide alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D- ...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)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-3DGlcpa1-3DManpa1-2DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2122h-1a_1-5]/1-1-2-3-3-3-4-4/a4-b1_b4-c1_c3-d1_d2-e1_e2-f1_f3-g1_g3-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(3+1)][a-D-Glcp]{[(3+1)][a-D-Glcp]{}}}}}}}}LINUCSPDB-CARE
#19: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#21: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 10 molecules

#20: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#22: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CryoEM structure of mEAK7 bound human V-ATPase complex
Type: COMPLEX / Entity ID: #1-#17 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24984 / Symmetry type: POINT

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