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- EMDB-81453: Focused map for area 3 of Vibrio cholerae Avs2 bound to phage ter... -

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Basic information

Entry
Database: EMDB / ID: EMD-81453
TitleFocused map for area 3 of Vibrio cholerae Avs2 bound to phage terminase
Map data
Sample
  • Complex: Vibrio cholerae Avs2 bound to phage terminase
    • Protein or peptide: VcAvs2
    • Protein or peptide: Terminase, large subunit
KeywordsBacterial immunity / MBL / Protease / ATPase / Terminase / Protein complex / ANTIVIRAL PROTEIN
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsHuang PP / Chen MR
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Focused map for area 3 of Vibrio cholerae Avs2 bound to phage terminase
Authors: Huang PP / Chen MR
History
DepositionJun 12, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_81453.png

Downloads & links

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Map

FileDownload / File: emd_81453.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 512 pix.
= 477.184 Å		0.93 Å/pix.
x 512 pix.
= 477.184 Å		0.93 Å/pix.
x 512 pix.
= 477.184 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.48017043 - 0.9118515
Average (Standard dev.)-0.00059509056 (±0.011999181)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 477.184 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_81453_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_81453_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vibrio cholerae Avs2 bound to phage terminase

EntireName: Vibrio cholerae Avs2 bound to phage terminase
Components
  • Complex: Vibrio cholerae Avs2 bound to phage terminase
    • Protein or peptide: VcAvs2
    • Protein or peptide: Terminase, large subunit

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Supramolecule #1: Vibrio cholerae Avs2 bound to phage terminase

SupramoleculeName: Vibrio cholerae Avs2 bound to phage terminase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)

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Macromolecule #1: VcAvs2

MacromoleculeName: VcAvs2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
SequenceString: MELQEIVFKI ECNGISGTAF FINKNRAITA YHNIVDHEKN NINCTLSCGR KFKANLSQKV TEHYKKLDVA LLELHDDFHF SENFSFTNY KKIENGTYWI SRGFPSAKKI SGDNILYGDN NIINQQLNHL RNYKIDLELE HSKKLSTYSG YSGSPLVINN S ISGIINQE ...String:
MELQEIVFKI ECNGISGTAF FINKNRAITA YHNIVDHEKN NINCTLSCGR KFKANLSQKV TEHYKKLDVA LLELHDDFHF SENFSFTNY KKIENGTYWI SRGFPSAKKI SGDNILYGDN NIINQQLNHL RNYKIDLELE HSKKLSTYSG YSGSPLVINN S ISGIINQE LLENGESKEL TALSIKYFID LLLSEDIDII EKDSSTYNPL RRTLSSEWFK RHIDKGVQDL GVRYTPAIHV KL DVENKID ALLKNKGFCS ESKTRFHNYL LSINKLIERL SGQTTFKKST NEYSKQSKLI NDINSSKEKT QRHFEEFCNN KYS HLNFNE LRSEAEIILK SIKILENILT ENGYSNEETK NAINASTSFL SYLENPDVNV LLANNPYLLL KGKAGTGKSH LLAD TILAQ QKNDIPAILL LGQHFTNDKS PWTQILSEIL RVEGTEHQFV SALNEIGQER RQRILFSIDA INEGKGKYFW PDHFI SFVN IFKQYPWICL VLTIRDTYLP KLVPKNISEK TEIITAKHIG FSGREQDAIK IFFNYYKINL PKIPYTSVEF SNPLFL KLF CEGLFCRGLH EIPEGYGGIS SVMNYFIDNI DEKLGHPKFY DYDSSGRVCR KIVHTLIKHK QSNEMSYILY DDACDIA NK IVEKYSNKKG FIEDLVHEGL LSKNLYWLDD GQDVEGVYFA YERLDDHFLA DFLAKNVIAK HNINNIFKPE GELFYLIQ K HYIYQGTIEA LSIILPELYE KDLFELVDEN YIESDEIVNA FINSLIWRKL DTIGEKTTKY VNEVVLKYEE SFQNFLDFM YVVAGDVNHP YNANKIHSML STMPLAIRDA EWTTRLKYSN EHDTYVSRLL EWVLKSDMHR SLSDDSALLT SISISWLLSS TTIDLRDKA TYALSNILIN RLNLGLNLIR IFHKIDDPYI HERIFAAVYG ATLNSENLSD LPNLANYIVD EIFQMEEVYP N VLIRDYAR NIVEYALYRG VVNLVDPEII RPPYNSNMPS SFPSNDETDS YKFNWDSEDF KQIHGSQNKI LSSMVTEYGR GV CCYGDFG RYTFQSALNL WKGIDPNLLS NYACKLIFEK FGYNVDIHGH FDRYANDGDR FENRVERIGK KYQWLSLYEV VAR VADNFK ITDWNDNEAG YYQGPWQNGL RNIDPTFPPH NDNREQLPIT INKIDFNSWS DDGGSWTTST DSLPDPKEMI VNGD FLSLE ASFSWSEPNQ LGIERENGER KQIWYQIRSY LVKEAEYETL KSWLKTQDFM GRWLPESSEN YSVFSKEHYW SPAYR DKVA DNEELHWQSI KKNRSDYSDN EIIADVLPTA EEHRWDDKNG TSFLAPRSEM FEGMSLSSSE IPSCWFNNNG QLACFD PHV FGEERSELMV NRSLLENFLN KNNLKILWTV LGEKQVLGST PKNNWIDISG VYYLSEDSVE GSTTVHLKEL GWKSKEN SN RVTPNFDFKE LLNTLKDSD

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Macromolecule #2: Terminase, large subunit

MacromoleculeName: Terminase, large subunit / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
SequenceString: MEQPINALND FHPLNEAGKI LIKHPSLAER KDEDGIHWIK SQWDGKWYPE KFSDYLRLHK IVKIPNNSDK PELFQTYKDK NNKRSRYMG LPNLKRANIK TQWTREMVEE WKKCRDDIVY FAETYCAITH IDYGVIKVQL RDYQRDMLKI MSSKRMTVCN L SRQLGKTT ...String:
MEQPINALND FHPLNEAGKI LIKHPSLAER KDEDGIHWIK SQWDGKWYPE KFSDYLRLHK IVKIPNNSDK PELFQTYKDK NNKRSRYMG LPNLKRANIK TQWTREMVEE WKKCRDDIVY FAETYCAITH IDYGVIKVQL RDYQRDMLKI MSSKRMTVCN L SRQLGKTT VVAIFLAHFV CFNKDKAVGI LAHKGSMSAE VLDRTKQAIE LLPDFLQPGI VEWNKGSIEL DNGSSIGAYA SS PDAVRGN SFAMIYIDEC AFIPNFHDSW LAIQPVISSG RRSKIIITTT PNGLNHFYDI WTAAVEGKSG FEPYTAIWNS VKE RLYNDE DIFDDGWQWS IQTINGSTLA QFRQEHTAAF EGTSGTLISG MKLAVMDFIE VTPDDHGFHR FKSPEPDRKY IATL DCSEG RGQDYHALHI IDVTDDVWEQ VGVLHSNTIS HLILPDIVMR YLVEYNECPV YIELNSTGVS VAKSLYMDLE YEGVI CDSY TDLGMKQTKR TKAVGCSTLK DLIEKDKLII HHRATIQEFR TFSEKGVSWA AEEGYHDDLV MSLVIFGWLS TQSKFI DYA DKDDMRLASE VFSKELQDMS DDYAPVIFVD SVHSAEYVPV SHGMSMV

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 178923
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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