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- EMDB-26909: Rat Kidney V-ATPase with SidK, State 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-26909
TitleRat Kidney V-ATPase with SidK, State 1
Map dataV-ATPase with SidK, State 1
Sample
  • Complex: Rat Kidney V-ATPase with SidK
    • Protein or peptide: x 17 types
  • Ligand: x 1 types
KeywordsV-ATPase / Complex / Membrane protein / PROTON TRANSPORT
Function / homology
Function and homology information


Metabolism of Angiotensinogen to Angiotensins / Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Insulin receptor recycling / RHOA GTPase cycle / eye pigmentation / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death ...Metabolism of Angiotensinogen to Angiotensins / Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Insulin receptor recycling / RHOA GTPase cycle / eye pigmentation / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death / plasma membrane proton-transporting V-type ATPase complex / rostrocaudal neural tube patterning / positive regulation of transforming growth factor beta1 production / cellular response to increased oxygen levels / proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase, V0 domain / synaptic vesicle lumen acidification / extrinsic component of synaptic vesicle membrane / intracellular organelle / clathrin-coated vesicle membrane / lysosomal lumen acidification / NURF complex / endosome to plasma membrane protein transport / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / head morphogenesis / vacuolar acidification / osteoclast development / protein localization to cilium / dendritic spine membrane / regulation of cellular pH / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase complex / microvillus / ATPase activator activity / regulation of MAPK cascade / MLL1 complex / autophagosome membrane / positive regulation of Wnt signaling pathway / cilium assembly / transmembrane transporter complex / regulation of macroautophagy / angiotensin maturation / ATP metabolic process / H+-transporting two-sector ATPase / axon terminus / ruffle / proton-transporting ATPase activity, rotational mechanism / RNA endonuclease activity / proton-transporting ATP synthase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / proton transmembrane transport / receptor-mediated endocytosis / secretory granule / terminal bouton / cilium / transmembrane transport / small GTPase binding / synaptic vesicle membrane / endocytosis / positive regulation of canonical Wnt signaling pathway / melanosome / synaptic vesicle / apical part of cell / signaling receptor activity / ATPase binding / cell body / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / positive regulation of ERK1 and ERK2 cascade / early endosome / lysosome / endosome membrane / endosome / apical plasma membrane / axon / external side of plasma membrane / lysosomal membrane / centrosome / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / extracellular space / nucleoplasm / ATP binding / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 protein / 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 ...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 protein / 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 / Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V1 complex, subunit F, eukaryotic / 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 N-term extension / 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
V-type proton ATPase subunit H / ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / V-type proton ATPase subunit G / Similar to RIKEN cDNA 1110020A23 / H(+)-transporting two-sector ATPase / V-type proton ATPase subunit S1 / V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase subunit F / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase 16 kDa proteolipid subunit c ...V-type proton ATPase subunit H / ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / V-type proton ATPase subunit G / Similar to RIKEN cDNA 1110020A23 / H(+)-transporting two-sector ATPase / V-type proton ATPase subunit S1 / V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase subunit F / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit e 2 / V-type proton ATPase subunit C 1 / V-type proton ATPase subunit / Type IV secretion protein Dot / Renin receptor / V-type proton ATPase subunit D / V-type proton ATPase subunit E 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Legionella pneumophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsRubinstein JL / Abbas YM
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Structure of V-ATPase with NCOA7B
Authors: Abbas YM / Rubinstein JL
History
DepositionMay 9, 2022-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26909.png

Downloads & links

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Map

FileDownload / File: emd_26909.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationV-ATPase with SidK, State 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.32 Å/pix.
x 340 pix.
= 449.65 Å		1.32 Å/pix.
x 340 pix.
= 449.65 Å		1.32 Å/pix.
x 340 pix.
= 449.65 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3225 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-45.496226999999998 - 70.45581
Average (Standard dev.)0.007812101 (±1.3380138)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 449.65 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Rat Kidney V-ATPase with SidK

EntireName: Rat Kidney V-ATPase with SidK
Components
  • Complex: Rat Kidney V-ATPase with SidK
    • Protein or peptide: ATPase H+-transporting V1 subunit A
    • Protein or peptide: V-type proton ATPase subunit B, brain isoform
    • Protein or peptide: V-type proton ATPase subunit C 1
    • Protein or peptide: ATPase H+-transporting V1 subunit D
    • Protein or peptide: V-type proton ATPase subunit E 1
    • Protein or peptide: V-type proton ATPase subunit F
    • Protein or peptide: V-type proton ATPase subunit G
    • Protein or peptide: V-type proton ATPase subunit H
    • Protein or peptide: Effector SidK
    • Protein or peptide: V-type proton ATPase 116 kDa subunit a isoform 1
    • Protein or peptide: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
    • Protein or peptide: V-type proton ATPase subunit S1
    • Protein or peptide: V-type proton ATPase subunit
    • Protein or peptide: V-type proton ATPase subunit e 2
    • Protein or peptide: Ribonuclease K
    • Protein or peptide: V-type proton ATPase 16 kDa proteolipid subunit
    • Protein or peptide: Renin receptor
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Rat Kidney V-ATPase with SidK

SupramoleculeName: Rat Kidney V-ATPase with SidK / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: ATPase H+-transporting V1 subunit A

MacromoleculeName: ATPase H+-transporting V1 subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: kidney
Molecular weightTheoretical: 68.341836 KDa
SequenceString: MDFSKLPKIR DEDKESTFGY VHGVSGPVVT ACDMAGAAMY ELVRVGHSEL VGEIIRLEGD MATIQVYEET SGVSVGDPVL RTGKPLSVE LGPGIMGAIF DGIQRPLSDI SSQTQSIYIP RGVNVSALSR DIKWEFIPSK NLRVGSHITG GDIYGIVNEN S LIKHKIML ...String:
MDFSKLPKIR DEDKESTFGY VHGVSGPVVT ACDMAGAAMY ELVRVGHSEL VGEIIRLEGD MATIQVYEET SGVSVGDPVL RTGKPLSVE LGPGIMGAIF DGIQRPLSDI SSQTQSIYIP RGVNVSALSR DIKWEFIPSK NLRVGSHITG GDIYGIVNEN S LIKHKIML PPRSRGSVTY IAPPGNYDAS DVVLELEFEG VKEKLSMVQV WPVRQVRPVT EKLPANHPLL TGQRVLDALF PC VQGGTTA IPGAFGCGKT VISQSLSKYS NSDVIIYVGC GERGNEMSEV LRDFPELTME VDGKVESIMK RTALVANTSN MPV AAREAS IYTGITLSEY FRDMGYHVSM MADSTSRWAE ALREISGRLA EMPADSGYPA YLGARLASFY ERAGRVKCLG NPER EGSVS IVGAVSPPGG DFSDPVTSAT LGIVQVFWGL DKKLAQRKHF PSVNWLISYS KYMRALDEYY DKHFTEFVPL RTKAK EILQ EEEDLAEIVQ LVGKASLAET DKITLEVAKL IKDDFLQQNG YTPYDRFCPF YKTVGMLSNM ISFYDMARRA VETTAQ SDN KITWSIIREH MGEILYKLSS MKFKDPVKDG EAKIKADYAQ LLEDMQNAFR SLED

UniProtKB: H(+)-transporting two-sector ATPase

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Macromolecule #2: V-type proton ATPase subunit B, brain isoform

MacromoleculeName: V-type proton ATPase subunit B, brain isoform / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: kidney
Molecular weightTheoretical: 56.61157 KDa
SequenceString: MALRAMRGIV NGAAPELPVP TGGPMAGARE QALAVSRNYL SQPRLTYKTV SGVNGPLVIL DHVKFPRYAE IVHLTLPDGT KRSGQVLEV SGSKAVVQVF EGTSGIDAKK TSCEFTGDIL RTPVSEDMLG RVFNGSGKPI DRGPVVLAED FLDIMGQPIN P QCRIYPEE ...String:
MALRAMRGIV NGAAPELPVP TGGPMAGARE QALAVSRNYL SQPRLTYKTV SGVNGPLVIL DHVKFPRYAE IVHLTLPDGT KRSGQVLEV SGSKAVVQVF EGTSGIDAKK TSCEFTGDIL RTPVSEDMLG RVFNGSGKPI DRGPVVLAED FLDIMGQPIN P QCRIYPEE MIQTGISAID GMNSIARGQK IPIFSAAGLP HNEIAAQICR QAGLVKKSKD VVDYSEENFA IVFAAMGVNM ET ARFFKSD FEENGSMDNV CLFLNLANDP TIERIITPRL ALTTAEFLAY QCEKHVLVIL TDMSSYAEAL REVSAAREEV PGR RGFPGY MYTDLATIYE RAGRVEGRNG SITQIPILTM PNDDITHPIP DLTGYITEGQ IYVDRQLHNR QIYPPINVLP SLSR LMKSA IGEGMTRKDH ADVSNQLYAC YAIGKDVQAM KAVVGEEALT SDDLLYLEFL QKFEKNFITQ GPYENRTVYE TLDIG WQLL RIFPKEMLKR IPQSTLSEFY PRDSAKH

UniProtKB: V-type proton ATPase subunit B, brain isoform

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Macromolecule #3: V-type proton ATPase subunit C 1

MacromoleculeName: V-type proton ATPase subunit C 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: kidney
Molecular weightTheoretical: 43.958453 KDa
SequenceString: MTEFWLISAP GEKTCQQTWE KLHAATTKNN NLAVSSKFNI PDLKVGTLDV LVGLSDELAK LDAFVEGVVK KVAQYMADVL EDSKDKVQE NLLASGVDLV TYITRFQWDM AKYPIKQSLK NISEIIAKGV TQIDNDLKSR ASAYNNLKGN LQNLERKNAG S LLTRSLAE ...String:
MTEFWLISAP GEKTCQQTWE KLHAATTKNN NLAVSSKFNI PDLKVGTLDV LVGLSDELAK LDAFVEGVVK KVAQYMADVL EDSKDKVQE NLLASGVDLV TYITRFQWDM AKYPIKQSLK NISEIIAKGV TQIDNDLKSR ASAYNNLKGN LQNLERKNAG S LLTRSLAE IVKKDDFVLD SEYLVTLLVV VPKLNHNDWI KQYETLAEMV VPRSSNVLSE DQDSYLCNVT LFKKAVDDFR HK ARENKFI VRDFQYNEEE MRADKEEMNR LSTDKKKQFG PLVRWLKVNF SEAFIAWIHI KALRVFVESV LRYGLPVNFQ AML LQPNKK SVKKLREVLH ELYKHLDSSA AAIIDAPMDI PGLNLSQQEY YPYVYYKIDC NLLEFK

UniProtKB: V-type proton ATPase subunit C 1

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Macromolecule #4: ATPase H+-transporting V1 subunit D

MacromoleculeName: ATPase H+-transporting V1 subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: kidney
Molecular weightTheoretical: 28.35902 KDa
SequenceString: MSGKDRIEIF PSRMAQTIMK ARLKGAQTGR NLLKKKSDAL TLRFRQILKK IIETKMLMGE VMREAAFSLA EAKFTAGDFS TTVIQNVNK AQVKIRAKKD NVAGVTLPVF EHYHEGTDSY ELTGLARGGE QLAKLKRNYA KAVELLVELA SLQTSFVTLD E AIKITNRR ...String:
MSGKDRIEIF PSRMAQTIMK ARLKGAQTGR NLLKKKSDAL TLRFRQILKK IIETKMLMGE VMREAAFSLA EAKFTAGDFS TTVIQNVNK AQVKIRAKKD NVAGVTLPVF EHYHEGTDSY ELTGLARGGE QLAKLKRNYA KAVELLVELA SLQTSFVTLD E AIKITNRR VNAIEHVIIP RIERTLAYII TELDEREREE FYRLKKIQEK KKIIKEKSEK DLERRRAAGE VMEPANLLAE EK DEDLLFE

UniProtKB: V-type proton ATPase subunit D

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Macromolecule #5: V-type proton ATPase subunit E 1

MacromoleculeName: V-type proton ATPase subunit E 1 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: kidney
Molecular weightTheoretical: 26.167453 KDa
SequenceString: MALSDADVQK QIKHMMAFIE QEANEKAEEI DAKAEEEFNI EKGRLVQTQR LKIMEYYEKK EKQIEQQKKI QMSNLMNQAR LKVLRARDD LITDLLNEAK QRLSKVVKDT TRYQVLLDGL VLQGLYQLLE PRMIVRCRKQ DFPLVKAAVQ KAIPMYKIAT K KDVDVQID ...String:
MALSDADVQK QIKHMMAFIE QEANEKAEEI DAKAEEEFNI EKGRLVQTQR LKIMEYYEKK EKQIEQQKKI QMSNLMNQAR LKVLRARDD LITDLLNEAK QRLSKVVKDT TRYQVLLDGL VLQGLYQLLE PRMIVRCRKQ DFPLVKAAVQ KAIPMYKIAT K KDVDVQID LEAYLPEDIA GGVEIYNGDR KIKVSNTLES RLDLIAQQMM PEVRGALFGA NANRKFLD

UniProtKB: V-type proton ATPase subunit E 1

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Macromolecule #6: V-type proton ATPase subunit F

MacromoleculeName: V-type proton ATPase subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: kidney
Molecular weightTheoretical: 13.389262 KDa
SequenceString:
MAGRGKLIAV IGDEDTVTGF LLGGIGELNK NRHPNFLVVE KDTTINEIED TFRQFLNRDD IGIILINQYI AEMVRHALDA HQRSIPAVL EIPSKEHPYD AAKDSILRRA KGMFTAEDLR

UniProtKB: V-type proton ATPase subunit F

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Macromolecule #7: V-type proton ATPase subunit G

MacromoleculeName: V-type proton ATPase subunit G / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: kidney
Molecular weightTheoretical: 13.733393 KDa
SequenceString:
MASQSQGIQQ LLQAEKRAAE KVSEARKRKN RRLKQAKEEA QAEIEQYRLQ REKEFKAKEA AALGSHGSCS SEVEKETQEK MTILQNYFE QNRDEVLDNL LAFVCDIRPE IHENYRING

UniProtKB: V-type proton ATPase subunit G

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Macromolecule #8: V-type proton ATPase subunit H

MacromoleculeName: V-type proton ATPase subunit H / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: kidney
Molecular weightTheoretical: 55.936949 KDa
SequenceString: MTKMDIRGAV DAAVPTNIIA AKAAEVRANK VNWQSYLQGQ MISAEDCEFI QRFEMKRCSE EKQEMLQTEG SQCAKTFINL MTHISKEQT VQYILTMVDD MLQENHQRVS IFFDYAKRSK STAWPYFLPM LNRQDPFTVH MAARIIAKLA AWGKELMEGS D LNYYFNWI ...String:
MTKMDIRGAV DAAVPTNIIA AKAAEVRANK VNWQSYLQGQ MISAEDCEFI QRFEMKRCSE EKQEMLQTEG SQCAKTFINL MTHISKEQT VQYILTMVDD MLQENHQRVS IFFDYAKRSK STAWPYFLPM LNRQDPFTVH MAARIIAKLA AWGKELMEGS D LNYYFNWI KTQLSSQKLR GSGVAVETGT ISASDSSQYV QCVAGCLQLM LRVNEYRFAW VEADGVNCIM GVLSNKCGFQ LQ YQMIFSI WLLAFSPQMC EHLRRYNIIP VLSDILQESV KEKVTRIILA AFRNFLEKST ERETRQEYAL AMIQCKVLKQ LEN LEQQKY DDEDISEDIK FLLEKLGESV QDLSSFDEYS SELKSGRLEW SPVHKSEKFW RENAVRLNEK NYELLKILTK LLEV SDDPQ VLAVAAHDVG EYVRHYPRGK RVIEQLGGKQ LVMNHMHHED QQVRYNALLA VQKLMVHNWE YLGKQLQSEQ PQTAA ARS

UniProtKB: V-type proton ATPase subunit H

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Macromolecule #9: Effector SidK

MacromoleculeName: Effector SidK / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 32.146178 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSFIKVGIKM GGLTSEQYHS QVVGKIGYIA RCMQTIDPEN NLKKIREDYQ DVLIWAEKNY RFEEILEASK SGKCPNDLDA LSRRSLILQ ELLRLVSSIS PFKMKLDLIE SQYEKMKQHV NLWKSDYHVK LNQLNQLTDY LKNAAPTPKN NFLRAMTSVL Q MQIAQYGI ...String:
MSFIKVGIKM GGLTSEQYHS QVVGKIGYIA RCMQTIDPEN NLKKIREDYQ DVLIWAEKNY RFEEILEASK SGKCPNDLDA LSRRSLILQ ELLRLVSSIS PFKMKLDLIE SQYEKMKQHV NLWKSDYHVK LNQLNQLTDY LKNAAPTPKN NFLRAMTSVL Q MQIAQYGI TEDNEGINQL FKLGLHLLAM ANEKIDEQYH LFKGYVKDQP EESPFEGILP AEDQKILVKT MIDYAMPKLS SK VLQDKLS ALSSSDVLTK TLLDSIDRIV KENEKLNALS KVK

UniProtKB: Type IV secretion protein Dot

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Macromolecule #10: V-type proton ATPase 116 kDa subunit a isoform 1

MacromoleculeName: V-type proton ATPase 116 kDa subunit a isoform 1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 96.429438 KDa
SequenceString: MGELFRSEEM TLAQLFLQSE AAYCCVSELE ELGKVQFRDL NPDVNVFQRK FVNEVRRCEE MDRKLRFVEK EIRKANIPIM DTGENPEVP FPRDMIDLEA NFEKIENELK EINTNQEALK RNFLELTELK FILRKTQQFF DEMADPDLLE ESSSLLEPNE M GRGAPLRL ...String:
MGELFRSEEM TLAQLFLQSE AAYCCVSELE ELGKVQFRDL NPDVNVFQRK FVNEVRRCEE MDRKLRFVEK EIRKANIPIM DTGENPEVP FPRDMIDLEA NFEKIENELK EINTNQEALK RNFLELTELK FILRKTQQFF DEMADPDLLE ESSSLLEPNE M GRGAPLRL GFVAGVINRE RIPTFERMLW RVCRGNVFLR QAEIENPLED PVTGDYVHKS VFIIFFQGDQ LKNRVKKICE GF RASLYPC PETPQERKEM ASGVNTRIDD LQMVLNQTED HRQRVLQAAA KNIRVWFIKV RKMKAIYHTL NLCNIDVTQK CLI AEVWCP VTDLDSIQFA LRRGTEHSGS TVPSILNRMQ TNQTPPTYNK TNKFTHGFQN IVDAYGIGTY REINPAPYTV ITFP FLFAV MFGDFGHGIL MTLFAVWMVL RESRILSQKN ENEMFSMVFS GRYIILLMGL FSIYTGLIYN DCFSKSLNIF GSSWS VRPM FTIGNWTEET LLGSSVLQLN PAIPGVFGGP YPFGIDPIWN IATNKLTFLN SFKMKMSVIL GIIHMLFGVS LSLFNH IYF KKPLNIYFGF IPEIIFMSSL FGYLVILIFY KWTAYDAHSS RNAPSLLIHF INMFLFSYPE SGNAMLYSGQ KGIQCFL IV VAMLCVPWML LFKPLILRHQ YLRKKHLGTL NFGGIRVGNG PTEEDAEIIQ HDQLSTHSED AEEPTEDEVF DFGDTMVH Q AIHTIEYCLG CISNTASYLR LWALSLAHAQ LSEVLWTMVI HIGLHVRSLA GGLGLFFIFA AFATLTVAIL LIMEGLSAF LHALRLHWVE FQNKFYTGTG FKFLPFSFEH IREGKFDE

UniProtKB: V-type proton ATPase 116 kDa subunit a 1

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Macromolecule #11: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a

MacromoleculeName: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 21.618553 KDa
SequenceString: MTGLELLYLG IFVAFWACMI VVGICYTIFD LGFRFDVAWF LTETSPFMWS NLGIGLAISL SVVGAAWGIY ITGSSIIGGG VKAPRIKTK NLVSIIFCEA VAIYGIIMAI VISNMAEPFS ATDPKAIGHR NYHAGYSMFG AGLTVGLSNL FCGVCVGIVG S GAALADAQ ...String:
MTGLELLYLG IFVAFWACMI VVGICYTIFD LGFRFDVAWF LTETSPFMWS NLGIGLAISL SVVGAAWGIY ITGSSIIGGG VKAPRIKTK NLVSIIFCEA VAIYGIIMAI VISNMAEPFS ATDPKAIGHR NYHAGYSMFG AGLTVGLSNL FCGVCVGIVG S GAALADAQ NPSLFVKILI VEIFGSAIGL FGVIVAILQT SRVKMGD

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

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Macromolecule #12: V-type proton ATPase subunit S1

MacromoleculeName: V-type proton ATPase subunit S1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 51.160359 KDa
SequenceString: MMAATVVSRI RTGTRWAPVL WLLLSLVAVA AAVAAEQQVP LVLWSSDRDL WAPVADTHEG HITSDMQLST YLDPALELGP RNVLLFLQD KLSIEDFTAY GGVFGNKQDS AFSNLENALD LAPSSLVLPA VDWYAISTLT TYLQEKLGAS PLHVDLATLK E LKLNASLP ...String:
MMAATVVSRI RTGTRWAPVL WLLLSLVAVA AAVAAEQQVP LVLWSSDRDL WAPVADTHEG HITSDMQLST YLDPALELGP RNVLLFLQD KLSIEDFTAY GGVFGNKQDS AFSNLENALD LAPSSLVLPA VDWYAISTLT TYLQEKLGAS PLHVDLATLK E LKLNASLP ALLLIRLPYT ASSGLMAPRE VLTGNDEVIG QVLSTLESED VPYTAALTAV RPSRVARDVA MVAGGLGRQL LQ TQVASPA IHPPVSYNDT APRILFWAQN FSVAYKDEWK DLTSLTFGVE NLNLTGSFWN DSFAMLSLTY EPLFGATVTF KFI LASRFY PVSARYWFTM ERLEIHSNGS VAHFNVSQVT GPSIYSFHCE YVSSLSKKGS LLVTNVPSLW QMTLHNFQIQ AFNV TGEQF SYASDCAGFF SPGIWMGLLT TLFMLFIFTY GLHMILSLKT MDRFDDRKGP TITLTQIV

UniProtKB: V-type proton ATPase subunit S1

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Macromolecule #13: V-type proton ATPase subunit

MacromoleculeName: V-type proton ATPase subunit / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 40.341934 KDa
SequenceString: MSFFPELYFN VDNGYLEGLV RGLKAGVLSQ ADYLNLVQCE TLEDLKLHLQ STDYGNFLAN EASPLTVSVI DDKLKEKMVV EFRHMRNHA YEPLASFLDF ITYSYMIDNV ILLITGTLHQ RSIAELVPKC HPLGSFEQME AVNIAQTPAE LYNAILVDTP L AAFFQDCI ...String:
MSFFPELYFN VDNGYLEGLV RGLKAGVLSQ ADYLNLVQCE TLEDLKLHLQ STDYGNFLAN EASPLTVSVI DDKLKEKMVV EFRHMRNHA YEPLASFLDF ITYSYMIDNV ILLITGTLHQ RSIAELVPKC HPLGSFEQME AVNIAQTPAE LYNAILVDTP L AAFFQDCI SEQDLDEMNI EIIRNTLYKA YLESFYKFCT LLGGTTADAM CPILEFEADR RAFIITINSF GTELSKEDRA KL FPHCGRL YPEGLAQLAR ADDYEQVKNV ADYYPEYKLL FEGAGSNPGD KTLEDRFFEH EVKLNKLAFL NQFHFGVFYA FVK LKEQEC RNIVWIAECI AQRHRAKIDN YIPIF

UniProtKB: V-type proton ATPase subunit

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Macromolecule #14: V-type proton ATPase subunit e 2

MacromoleculeName: V-type proton ATPase subunit e 2 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 9.20302 KDa
SequenceString:
MTAHSFALPV IIFTTFWGLI GIAGPWFVPK GPNRGVIITM LVATAVCCYL FWLIAILAQL NPLFGPQLKN ETIWYVRFLW E

UniProtKB: V-type proton ATPase subunit e 2

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Macromolecule #15: Ribonuclease K

MacromoleculeName: Ribonuclease K / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 11.000004 KDa
SequenceString:
MASLLCCGPK LAACGIVLSA WGVIMLIMLG IFFNVHSAVL IEDVPFTEKD FENGPQNIYN LYEQVSYNCF IAAGLYLLLG GFSFCQVRL NKRKEYMVR

UniProtKB: Similar to RIKEN cDNA 1110020A23

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Macromolecule #16: V-type proton ATPase 16 kDa proteolipid subunit

MacromoleculeName: V-type proton ATPase 16 kDa proteolipid subunit / type: protein_or_peptide / ID: 16 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 15.815833 KDa
SequenceString:
MADIKNNPEY SSFFGVMGAS SAMVFSAMGA AYGTAKSGTG IAAMSVMRPE LIMKSIIPVV MAGIIAIYGL VVAVLIANSL TDGITLYRS FLQLGAGLSV GLSGLAAGFA IGIVGDAGVR GTAQQPRLFV GMILILIFAE VLGLYGLIVA LILSTK

UniProtKB: V-type proton ATPase 16 kDa proteolipid subunit c

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Macromolecule #17: Renin receptor

MacromoleculeName: Renin receptor / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 39.118578 KDa
SequenceString: MAVLVVLLSS LVSSALANEF SILRSPGSVV FRNGNWPIPG DRIPDVAALS MGFSVKEDLS WPGLAVGNLF HRPRATIMVT VKGVDKLAL PTGSVISYPL ENAVPFSLDS VANSIHSLFS EETPVVLQLA PSEERVYMVG KANSVFEDLS VTLRQLRNRL F QENSVLNS ...String:
MAVLVVLLSS LVSSALANEF SILRSPGSVV FRNGNWPIPG DRIPDVAALS MGFSVKEDLS WPGLAVGNLF HRPRATIMVT VKGVDKLAL PTGSVISYPL ENAVPFSLDS VANSIHSLFS EETPVVLQLA PSEERVYMVG KANSVFEDLS VTLRQLRNRL F QENSVLNS LPLNSLSRNN EVDLLFLSEL QVLHDISSLL SRHKHLAKDH SPDLYSLELA GLDELGKRYG EDSEQFRDAS RI LVDALQK FADDMYSLYG GNAVVELVTV KSFDTSLVRK SRTILETKQE NTQSPYNLAY KYNLEYSVVF NLVLWIMTGL ALA VIITSY NIWNMDPGYD SIIYRMTNQK IRMD

UniProtKB: Renin receptor

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Macromolecule #18: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 18 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 44.825 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 0.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER
Details: Model-map FSC (threshold 0.5) calculated in phenix.validation_cryoem
Number images used: 45083
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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