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- EMDB-8462: Thermus thermophilus V/A-ATPase bound to VH dAbs -

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Basic information

Entry
Database: EMDB / ID: EMD-8462
TitleThermus thermophilus V/A-ATPase bound to VH dAbs
Map dataThermus thermophilus V/A-ATPase bound to VH dAb
Sample
  • Complex: Thermus thermophilus V/A-ATPase bound to VH dAbs
    • Protein or peptide: V-type ATP synthase alpha chain
    • Protein or peptide: V-type ATP synthase beta chain
    • Protein or peptide: V-type ATP synthase subunit E
    • Protein or peptide: V-type ATPase subunit GV-ATPase
    • Protein or peptide: V-type ATP synthase subunit D
    • Protein or peptide: V-type ATP synthase subunit F
    • Protein or peptide: V-type ATP synthase subunit C
    • Protein or peptide: Archaeal/vacuolar-type H+-ATPase subunit I
    • Protein or peptide: Vacuolar type ATP synthase subunit
    • Protein or peptide: Human heavy chain domain antibody
KeywordsV/A-ATPase / membrane protein / complex / antibody / HYDROLASE
Function / homology
Function and homology information


proton-transporting V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding / metal ion binding
Similarity search - Function
V-type ATP synthase subunit I, N-terminal / Vacuolar ATPase subunit I, N-terminal proximal lobe / Vacuolar ATPase Subunit I N-terminal proximal lobe / V-type ATPase subunit I, N-terminal domain / ATPase, V0 complex, c subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit F, bacterial/archaeal / V-ATPase proteolipid subunit / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d ...V-type ATP synthase subunit I, N-terminal / Vacuolar ATPase subunit I, N-terminal proximal lobe / Vacuolar ATPase Subunit I N-terminal proximal lobe / V-type ATPase subunit I, N-terminal domain / ATPase, V0 complex, c subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit F, bacterial/archaeal / V-ATPase proteolipid subunit / 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-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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Uncharacterized protein / V-type ATP synthase subunit I / V-type ATP synthase subunit D / F0F1 ATP synthase subunit C / V-type ATP synthase subunit E / V-type ATP synthase subunit C / V-type ATP synthase subunit F / V-type ATP synthase alpha chain / V-type ATP synthase beta chain / V-type ATP synthase, subunit (VAPC-THERM) ...Uncharacterized protein / V-type ATP synthase subunit I / V-type ATP synthase subunit D / F0F1 ATP synthase subunit C / V-type ATP synthase subunit E / V-type ATP synthase subunit C / V-type ATP synthase subunit F / V-type ATP synthase alpha chain / V-type ATP synthase beta chain / V-type ATP synthase, subunit (VAPC-THERM) / V-type ATP synthase subunit I / V-type ATP synthase, subunit K / V-type ATP synthase beta chain / V-type ATP synthase subunit D
Similarity search - Component
Biological speciesHomo sapiens (human) / Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsDavies RB / Smits C / Wong ASW / Stock D / Sandin S / Stewart AG
Funding support Australia, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1022143 Australia
National Health and Medical Research Council (NHMRC, Australia)1047004 Australia
CitationJournal: J Struct Biol / Year: 2017
Title: Cryo-EM analysis of a domain antibody bound rotary ATPase complex.
Authors: Roberta B Davies / Callum Smits / Andrew S W Wong / Daniela Stock / Mary Christie / Sara Sandin / Alastair G Stewart /
Abstract: The bacterial A/V-type ATPase/synthase rotary motor couples ATP hydrolysis/synthesis with proton translocation across biological membranes. The A/V-type ATPase/synthase from Thermus thermophilus has ...The bacterial A/V-type ATPase/synthase rotary motor couples ATP hydrolysis/synthesis with proton translocation across biological membranes. The A/V-type ATPase/synthase from Thermus thermophilus has been extensively studied both structurally and functionally for many years. Here we provide an 8.7Å resolution cryo-electron microscopy 3D reconstruction of this complex bound to single-domain antibody fragments, small monomeric antibodies containing just the variable heavy domain. Docking of known structures into the density revealed the molecular orientation of the domain antibodies, suggesting that structure determination of co-domain antibody:protein complexes could be a useful avenue for unstable or smaller proteins. Although previous studies suggested that the presence of fluoroaluminate in this complex could change the rotary state of this enzyme, we observed no gross structural rearrangements under these conditions.
History
DepositionOct 29, 2016-
Header (metadata) releaseNov 9, 2016-
Map releaseFeb 1, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5tsj
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8462.png

Downloads & links

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Map

FileDownload / File: emd_8462.map.gz / Format: CCP4 / Size: 21.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThermus thermophilus V/A-ATPase bound to VH dAb
Voxel sizeX=Y=Z: 1.91 Å
Density
Contour LevelBy EMDB: 0.109 / Movie #1: 0.1
Minimum - Maximum-0.061157163 - 0.22807963
Average (Standard dev.)-0.000024600811 (±0.023184929)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions178178178
Spacing178178178
CellA=B=C: 339.97998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.911.911.91
M x/y/z178178178
origin x/y/z0.0000.0000.000
length x/y/z339.980339.980339.980
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS178178178
D min/max/mean-0.0610.228-0.000

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Supplemental data

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Sample components

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Entire : Thermus thermophilus V/A-ATPase bound to VH dAbs

EntireName: Thermus thermophilus V/A-ATPase bound to VH dAbs
Components
  • Complex: Thermus thermophilus V/A-ATPase bound to VH dAbs
    • Protein or peptide: V-type ATP synthase alpha chain
    • Protein or peptide: V-type ATP synthase beta chain
    • Protein or peptide: V-type ATP synthase subunit E
    • Protein or peptide: V-type ATPase subunit GV-ATPase
    • Protein or peptide: V-type ATP synthase subunit D
    • Protein or peptide: V-type ATP synthase subunit F
    • Protein or peptide: V-type ATP synthase subunit C
    • Protein or peptide: Archaeal/vacuolar-type H+-ATPase subunit I
    • Protein or peptide: Vacuolar type ATP synthase subunit
    • Protein or peptide: Human heavy chain domain antibody

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Supramolecule #1: Thermus thermophilus V/A-ATPase bound to VH dAbs

SupramoleculeName: Thermus thermophilus V/A-ATPase bound to VH dAbs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: V-type ATP synthase alpha chain

MacromoleculeName: V-type ATP synthase alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 63.628902 KDa
SequenceString: MIQGVIQKIA GPAVIAKGML GARMYDICKV GEEGLVGEII RLDGDTAFVQ VYEDTSGLKV GEPVVSTGLP LAVELGPGML NGIYDGIQR PLERIREKTG IYITRGVVVH ALDREKKWAW TPMVKPGDEV RGGMVLGTVP EFGFTHKILV PPDVRGRVKE V KPAGEYTV ...String:
MIQGVIQKIA GPAVIAKGML GARMYDICKV GEEGLVGEII RLDGDTAFVQ VYEDTSGLKV GEPVVSTGLP LAVELGPGML NGIYDGIQR PLERIREKTG IYITRGVVVH ALDREKKWAW TPMVKPGDEV RGGMVLGTVP EFGFTHKILV PPDVRGRVKE V KPAGEYTV EEPVVVLEDG TELKMYHTWP VRRARPVQRK LDPNTPFLTG MRILDVLFPV AMGGTAAIPG PFGSGKTVTQ QS LAKWSNA DVVVYVGCGE RGNEMTDVLV EFPELTDPKT GGPLMHRTVL IANTSNMPVA AREASIYVGV TIAEYFRDQG FSV ALMADS TSRWAEALRE ISSRLEEMPA EEGYPPYLAA RLAAFYERAG KVITLGGEEG AVTIVGAVSP PGGDMSEPVT QSTL RIVGA FWRLDASLAF RRHFPAINWN GSYSLFTSAL DPWYRENVAE DYPELRDAIS ELLQREAGLQ EIVQLVGPDA LQDAE RLVI EVGRIIREDF LQQNAYHEVD AYCSMKKAYG IMKMILAFYK EAEAAIKRGV SIDEILQLPV LERIGRARYV SEEEFP AYF EEAMKEIQGA FKAL

UniProtKB: V-type ATP synthase alpha chain

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Macromolecule #2: V-type ATP synthase beta chain

MacromoleculeName: V-type ATP synthase beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 50.850738 KDa
SequenceString: EYTGITYISG PLLFVENAKD LAYGAIVDIK DGTGRVRGGQ VIEVSEEYAV IQVFEETTGL DLATTSVSLV EDVARLGVSK EMLGRRFNG IGKPIDGLPP ITPEKRLPIT GLPLNPVARR KPEQFIQTGI STIDVMNTLV RGQKLPIFSG SGLPANEIAA Q IARQATVR ...String:
EYTGITYISG PLLFVENAKD LAYGAIVDIK DGTGRVRGGQ VIEVSEEYAV IQVFEETTGL DLATTSVSLV EDVARLGVSK EMLGRRFNG IGKPIDGLPP ITPEKRLPIT GLPLNPVARR KPEQFIQTGI STIDVMNTLV RGQKLPIFSG SGLPANEIAA Q IARQATVR PDLSGEGEKE EPFAVVFAAM GITQRELSYF IQEFERTGAL SRSVLFLNKA DDPTIERILT PRMALTVAEY LA FEHDYHV LVILTDMTNY CEALREIGAA REEIPGRRGY PGYMYTDLAT IYERAGVVEG KKGSVTQIPI LSMPDDDRTH PIP DLTGYI TEGQIQLSRE LHRKGIYPPI DPLPSLSRLM NNGVGKGKTR EDHKQVSDQL YSAYANGVDI RKLVAIIGED ALTE NDRRY LQFADAFERF FINQGQQNRS IEESLQIAWA LLSMLPQGEL KRISKDHIGK YY

UniProtKB: V-type ATP synthase beta chain

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Macromolecule #3: V-type ATP synthase subunit E

MacromoleculeName: V-type ATP synthase subunit E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 20.481418 KDa
SequenceString:
KLEAILSQEV EAEIQALLQE AEAKAEAVKR EAEEKAKALL QARERALEAQ YRAALRRAES AGELLVATAR TQARGEVLEE VRRRVREAL EALPQKPEWP EVVRKLALEA LEALPGAKAL VANPEDLPHL EAMARERGVE LQAEPALRLG VRAVGAEGKT Q VENSLLAR MDRAWDAMSS KVAQALWG

UniProtKB: V-type ATP synthase subunit E

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Macromolecule #4: V-type ATPase subunit G

MacromoleculeName: V-type ATPase subunit G / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 11.752551 KDa
SequenceString:
GMGGLGLIKS LAEKEKQLLE RLEAAKKEAE ERVKRAEAEA KALLEEAEAK AKALEAQYRE RERAETEALL ARYRERAEAE AKAVREKAM ARLDEAVALV LKEVLP

UniProtKB: Uncharacterized protein

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Macromolecule #5: V-type ATP synthase subunit D

MacromoleculeName: V-type ATP synthase subunit D / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 23.350973 KDa
SequenceString: SQVSPTRMNL LQRRGQLRLA QKGVDLLKKK RDALVAEFFG LVREAMEARK ALDQAAKEAY AALLLAQAFD GPEVVAGAAL GVPPLEGVE AEVENVWGSK VPRLKATFPD GALLSPVGTP AYTLEASRAF RRYAEALIRV ANTETRLKKI GEEIKKTTRR V NALEQVVI ...String:
SQVSPTRMNL LQRRGQLRLA QKGVDLLKKK RDALVAEFFG LVREAMEARK ALDQAAKEAY AALLLAQAFD GPEVVAGAAL GVPPLEGVE AEVENVWGSK VPRLKATFPD GALLSPVGTP AYTLEASRAF RRYAEALIRV ANTETRLKKI GEEIKKTTRR V NALEQVVI PGIRAQIRFI QQVLEQRERE DTFRLKRIKG KIEAREAEEE GG

UniProtKB: V-type ATP synthase subunit D

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Macromolecule #6: V-type ATP synthase subunit F

MacromoleculeName: V-type ATP synthase subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 10.824321 KDa
SequenceString:
MAVIADPETA QGFRLAGLEG YGASSAEEAQ SLLETLVERG GYALVAVDEA LLPDPERAVE RLMRGRDLPV LLPIAGLKEA FQGHDVEGY MRELVRKTIG F

UniProtKB: V-type ATP synthase subunit F

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Macromolecule #7: V-type ATP synthase subunit C

MacromoleculeName: V-type ATP synthase subunit C / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 35.96857 KDa
SequenceString: MADDFAYLNA RVRVRRGTLL KESFFQEALD LSFADFLRLL SETVYGGELA GQGLPDVDRA VLRTQAKLVG DLPRLVTGEA REAVRLLLL RNDLHNLQAL LRAKATGRPF EEVLLLPGTL REEVWRQAYE AQDPAGMAQV LAVPGHPLAR ALRAVLRETQ D LARVEALL ...String:
MADDFAYLNA RVRVRRGTLL KESFFQEALD LSFADFLRLL SETVYGGELA GQGLPDVDRA VLRTQAKLVG DLPRLVTGEA REAVRLLLL RNDLHNLQAL LRAKATGRPF EEVLLLPGTL REEVWRQAYE AQDPAGMAQV LAVPGHPLAR ALRAVLRETQ D LARVEALL AKRFFEDVAK AAKGLDQPAL RDYLALEVDA ENLRTAFKLQ GSGLAPDAFF LKGGRFVDRV RFARLMEGDY AV LDELSGT PFSGLSGVRD LKALERGLRC VLLKEAKKGV QDPLGVGLVL AYVKEREWEA VRLRLLARRA YFGLPRAQVE EEV VCP

UniProtKB: V-type ATP synthase subunit C

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Macromolecule #8: Archaeal/vacuolar-type H+-ATPase subunit I

MacromoleculeName: Archaeal/vacuolar-type H+-ATPase subunit I / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 72.272453 KDa
SequenceString: MIAPMEKLVL AGPKGRAKEL LQSLQQAGVV HLETLRPEAL SAYQLSPEER AELRRWEAVS AGAEHTLSLL GLEAEPARPF PEGLEAAEK ALSPIQAHAE GLTRQKQELE EELALAQAYL EPLERLAALA HGLDKSPFLR VIPFLLTEKE LPLVEEALRK A LEDRYLLA ...String:
MIAPMEKLVL AGPKGRAKEL LQSLQQAGVV HLETLRPEAL SAYQLSPEER AELRRWEAVS AGAEHTLSLL GLEAEPARPF PEGLEAAEK ALSPIQAHAE GLTRQKQELE EELALAQAYL EPLERLAALA HGLDKSPFLR VIPFLLTEKE LPLVEEALRK A LEDRYLLA HEAYAGGVPA LVVVHRKEVD QAKAALSRAG VAELRLPGAL GELPLSEAAR RLKERAEAAP RELSEVRQHL AK LARESAS TLQSLWTRAQ DEVARLKALE ELASGRFGFA LLGYVPVKAK PKVEEALARH KENVVYAFEP VDEHHEADRI PVV LDNPPW VKPFELLVSF LNTPKYGTFD PTPVVPIFFP FWFGMIVGDI GYALLFYLVG RWLSGYVKRN EPLVIDLFAL KLKP PVLAK LVYILNWMVF WTVVWGLIYG EFFGTFLEHL GVFGTPEHPG LIPILIHRID TAKTANLLIL LSVAFGVVMV FAGLI LRAY LGLKHRHMAH FWEGVGYLGG LLGILALAAS YLGNLQAGWL SALMYLGFGV FLLSVVMSSI WLMIPEIFTQ AGHILS HIR IYAVGAAGGI LAGLLTDVGF AMAERLGLIG VLLGIVVAGV LHLLILLLTT LGHMLQPIRL IWVEFFTKFG FYEENGR PY RPFKSVRETQ

UniProtKB: V-type ATP synthase subunit I

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Macromolecule #9: Vacuolar type ATP synthase subunit

MacromoleculeName: Vacuolar type ATP synthase subunit / type: protein_or_peptide / ID: 9 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 9.841714 KDa
SequenceString:
MKKLLVTVLL AVFGALAFAA EEAAASGGLD RGLIAVGMGL AVGLAALGTG VAQARIGAAG VGAIAEDRSN FGTALIFLLL PETLVIFGL LIAFILNGRL

UniProtKB: F0F1 ATP synthase subunit C

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Macromolecule #10: Human heavy chain domain antibody

MacromoleculeName: Human heavy chain domain antibody / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.345025 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
STEVQLLESG GGLVQPGGSL RLSCAASGFT FSTYMMSWVR QAPGKGLEWV SSIEGSGSKT YYADSVKGRF TISRDNSKNT LYLQMNSLR AEDTAVYYCA KRDSSFGFDY WGQGTLVTVS SAAALEIKRA SQPELAPEDP EDVEHHHHHH

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 13.8 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

8016

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61045
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-5tsj:
Thermus thermophilus V/A-ATPase bound to VH dAbs

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