EMDB-34438: Near-atomic structure of five-fold averaged PBCV-1 capsid

Basic information

Entry

Database: EMDB / ID: EMD-34438

• Title: Near-atomic structure of five-fold averaged PBCV-1 capsid

Sample

• Virus: Paramecium bursaria Chlorella virus 1
  • Protein or peptide: x 26 types

• Keywords: giant virus / nucleocytoplasmic large DNA viruses (NCLDVs) / viral assembly / Paramecium bursaria chlorella virus 1 (PBCV-1) / chlorovirus / major capsid protein / minor capsid protein / VIRUS / VIRAL PROTEIN

Function / homology

Function:

viral capsid / lipid binding / virion membrane / structural molecule activity / membrane

Domain/homology:

Chlorovirus glycoprotein repeat / Domain of unknown function DUF5901 / Chlorovirus glycoprotein repeat / Family of unknown function (DUF5901) / Protein of unknown function DUF5762 / Protein of unknown function DUF5761 / Domain of unknown function DUF5899 / : / Minor capsid protein P8 central region / Minor capsid protein P9 transmembrane helices / Minor capsid protein P2, DUF5899 / Minor capsid protein P11, C-terminal conserved region / Peptidase G2, IMC autoproteolytic cleavage domain / Peptidase_G2, IMC autoproteolytic cleavage domain / Major capsid protein, N-terminal / Major capsid protein N-terminus / Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein / Parallel beta-helix repeat / Parallel beta-helix repeats

Component:

Major capsid protein VP54 / DUF5901 domain-containing protein / Capsid protein / Minor capsid protein P4 / Capsid protein / Minor capsid protein P8 / Major capsid protein / Peptidase G2 IMC autoproteolytic cleavage domain-containing protein / Minor capsid protein P12 / Minor capsid protein P6 / Uncharacterized protein / Capsid protein / Uncharacterized protein / Minor capsid protein P2 / Minor capsid protein P11 / Capsid protein / Capsid protein / Chlorovirus glycoprotein repeat domain-containing protein / Chlorovirus glycoprotein repeat domain-containing protein / Chlorovirus glycoprotein repeat domain-containing protein / Minor capsid protein P9 / Minor capsid protein P13 / Uncharacterized protein / Uncharacterized protein / Minor capsid protein 3 / Minor capsid protein P5

• Biological species: Paramecium bursaria Chlorella virus 1
• Method: single particle reconstruction / cryo EM / Resolution: 3.8 Å
• Authors: Shao Q / Agarkova IV / Noel EA / Dunigan DD / Liu Y / Wang A / Guo M / Xie L / Zhao X / Rossmann MG / Van Etten JL / Klose T / Fang Q

Funding support

United States, 2 items

Organization	Grant number	Country
National Science Foundation (NSF, United States)	1736030	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI011219	United States

• Citation: Journal: Nat Commun / Year: 2022; Title: Near-atomic, non-icosahedrally averaged structure of giant virus Paramecium bursaria chlorella virus 1.; Authors: Qianqian Shao / Irina V Agarkova / Eric A Noel / David D Dunigan / Yunshu Liu / Aohan Wang / Mingcheng Guo / Linlin Xie / Xinyue Zhao / Michael G Rossmann / James L Van Etten / Thomas Klose / Qianglin Fang / ; Abstract: Giant viruses are a large group of viruses that infect many eukaryotes. Although components that do not obey the overall icosahedral symmetry of their capsids have been observed and found to play critical roles in the viral life cycles, identities and high-resolution structures of these components remain unknown. Here, by determining a near-atomic-resolution, five-fold averaged structure of Paramecium bursaria chlorella virus 1, we unexpectedly found the viral capsid possesses up to five major capsid protein variants and a penton protein variant. These variants create varied capsid microenvironments for the associations of fibers, a vesicle, and previously unresolved minor capsid proteins. Our structure reveals the identities and atomic models of the capsid components that do not obey the overall icosahedral symmetry and leads to a model for how these components are assembled and initiate capsid assembly, and this model might be applicable to many other giant viruses.

History

Deposition	Oct 6, 2022	-
Header (metadata) release	Nov 16, 2022	-
Map release	Nov 16, 2022	-
Update	Sep 6, 2023	-
Current status	Sep 6, 2023	Processing site: PDBj / Status: Released

Map

• File: Download / File: emd_34438.map.gz / Format: CCP4 / Size: 6.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.62 Å

Density

Contour Level	By AUTHOR: 0.55
Minimum - Maximum	-1.5407423 - 2.269498
Average (Standard dev.)	0.0007873746 (±0.09836302)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin -600 -600 -600 Dimensions 1200 1200 1200 Spacing 1200 1200 1200
Cell	A=B=C: 1944.0 Å α=β=γ: 90.0 °

Supplemental data

Sample components

Entire : Paramecium bursaria Chlorella virus 1

• Entire: Name: Paramecium bursaria Chlorella virus 1

Components

• Virus: Paramecium bursaria Chlorella virus 1
  • Protein or peptide: Major capsid protein (MCP)
  • Protein or peptide: MCPv1
  • Protein or peptide: MCPv2
  • Protein or peptide: MCPv3
  • Protein or peptide: MCPv4
  • Protein or peptide: P1v1
  • Protein or peptide: P2
  • Protein or peptide: P3
  • Protein or peptide: P4
  • Protein or peptide: P5
  • Protein or peptide: P6
  • Protein or peptide: P8
  • Protein or peptide: P9
  • Protein or peptide: P11
  • Protein or peptide: P12
  • Protein or peptide: P13
  • Protein or peptide: P15
  • Protein or peptide: P16
  • Protein or peptide: P17
  • Protein or peptide: P18
  • Protein or peptide: P19
  • Protein or peptide: P20
  • Protein or peptide: P21
  • Protein or peptide: MCPv5
  • Protein or peptide: P22
  • Protein or peptide: P23

Supramolecule #1: Paramecium bursaria Chlorella virus 1

• Supramolecule: Name: Paramecium bursaria Chlorella virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10506 / Sci species name: Paramecium bursaria Chlorella virus 1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

Macromolecule #1: Major capsid protein (MCP)

• Macromolecule: Name: Major capsid protein (MCP) / type: protein_or_peptide / ID: 1 / Number of copies: 72 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 48.199625 KDa

Sequence

String:

MAGGLSQLVA YGAQDVYLTG NPQITFFKTV YRRYTNFAIE SIQQTINGSV GFGNKVSTQI SRNGDLITDI VVEFVLTKGG NGGTTYYPA EELLQDVELE IGGQRIDKHY NDWFRTYDAL FRMNDDRYNY RRMTDWVNNE LVGAQKRFYV PLIFFFNQTP G LALPLIAL QYHEVKLYFT LASQVQGVNY NGSSAIAGAA QPTMSVWVDY IFLDTQERTR FAQLPHEYLI EQLQFTGSET AT PSATTQA SQNIRLNFNH PTKYLAWNFN NPTNYGQYTA LANIPGACSG AGTAAATVTT PDYGNTGTYN EQLAVLDSAK IQL NGQDRF ATRKGSYFNK VQPYQSIGGV TPAGVYLYSF ALKPAGRQPS GTCNFSRIDN ATLSLTYKTC SIDATSPAAV LGNT ETVTA NTATLLTALN IYAKNYNVLR IMSGMGGLAY AN

UniProtKB: Major capsid protein

Macromolecule #2: MCPv1

• Macromolecule: Name: MCPv1 / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 58.136645 KDa

Sequence

String:

MPGAISQLVS YGAQDVYLTG NPQITFFKAV YRRYTNFAME SIQQTFDGTT DFGKFPTVTI SRNGDLAGPI WIEVNLPSLL GYNITPTPA EGNTSNIAAI STVFKDDYNN YWWTYNPGTT PQYSNLIAAF SNVDYKYYAN AVTSTYPPTA LSNVVYSWPY M ITGNTGTR STVAIPTANL RYVNGIGLAL FNSIELELGG QRIDKHYSEW WDIWTELTET AEKIQGYNTM VGRYDPAVYN AG WNISQAQ GGTYYVPLKF CYNRNPGLYM PLVALSYHQM KLNFNINNYL NCVKCNYPVT ALTSKNGANP LSITNMKLYT DFV FLDAPE RIRMSEIQHE YLVTQLQWQG SEPVTAPGDP NGSTNRKITL NFNHPVRELV FVYQAASNYD VDAVTGNNIF DYEI PANPT ATPPYAGGGE VFTEVKLIIN GSDRFSGRPG AYFRLVQPYE HHVRVPSKSV YVYSFALEDA DSRQPNGSAN FTRYD SVQL QLTLNENLAS GRVQIYAPNF NILRIAAGMG GLAFAN

UniProtKB: Capsid protein

Macromolecule #3: MCPv2

• Macromolecule: Name: MCPv2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 55.733863 KDa

Sequence

String:

MDPTTRFRGS DVPVHNEDHM VFAKPSEIGL QGRQGFYTNT NVVTNTYNHV YTPPGGHTGG KFTQDIYTTD LLIAAKDEKA DKIPLDKRM DGTFSEGTFV QLLSRGPQDV YLTYNPQISL FKRKYKRYTN FAIENFEERF STVVKFGTRN ICQLSKNGDL I GNMCFRVT LPNLGIPGGT WAPTMGYNIF STIRMRIGDT IVQSHDRVWY DIDDKMFCDS TKIQGLDELI KRNVTLTTDQ EW ELIIPLK FFCCKRNTGK QQFLPILNMD TNINVYLEFN LLPLNSLVTL PTGSILPDIQ SIDASVWVDY IFLDDTEKFR FAQ DPCVYL IEQTASMDSL SYATTTSGQT YNKTDVYVDM KELNKPVKYV EIIAYEQGST SFDYVDIIES ATFYLNSDEQ FKTR AGEYF SLVQPYQHFK RSDPTSNIST FSFALDAGSF QPNGYLNFAP YVRTRFAFKI QPQTTPHVIR LFAVCLNWVK FESGL VKLL FN

UniProtKB: Major capsid protein VP54

Macromolecule #4: MCPv3

• Macromolecule: Name: MCPv3 / type: protein_or_peptide / ID: 4 / Number of copies: 11 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 45.115641 KDa

Sequence

String:

MSGALNQLVA VGKQDAFITG DNLDNSVWRN VTKKVSNFAM ESIENYINVN PGSTTSIVVG RFGDLVRKVT LEITMKKGST TNPFYPSEQ YVKYAHLSIG GQIVYRIDDF PTWTRVHEEL FMDPDTRATN QRVNNFRPED PVGAIRKFYL DIPLFFTDDA S KALPLIAL QYHEVKLDVL FASPGDIPGI DASYTPTVEC YIDYVFLDTP EREWFARNTH MYVIEQLQHY NNVFSVAAVE QT KRLNLPF TMPTRYLIWL LKTGADGVYT TSGYPFENND SYAAIKSAKL QFNGTDRFSE RPGYYFTTVQ PQDAFGRSPS AGI YVYSFG LDVTGMTSKG ALNFSRMDNA TLSITTKAAT AATISDVYNQ STTLASAITD FTSIAIYAKS FNVLKIDYGM GGML FAN

UniProtKB: Capsid protein

Macromolecule #5: MCPv4

• Macromolecule: Name: MCPv4 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 45.034797 KDa

Sequence

String:

MVSGGVVQLI SYGAQDVYIS GGPKTIFKSY VKKVNNFAID SVKIPINGMG NGNPSVLIPR NGDLIKSIRL EITLKKGTGQ SFYPAEQLI SYLALKIGGN IIQKIDDFSN FCRIRNELFM DPDERHTDYR VNNFSSSDVV GSVKYFFLDL PLFFSKDTSV A LPLIALQY HDIELDFRFN DVSTIQGVDA SYTPTIEMYI DYVYLEQQER IKLVEKPLFY NIEQCNFYRK DITFPALSST FK LDIPFNN PSRFLVWYFN TDSFGIYNTS GLYFNSNDAA APLESAVMLL NGTERFKSRE GMYFNCVQPQ QALGRSPSSG IYM YAFGED VANATSKGAL DMSRVNELSL QLTTKNATAA NVYTVYNPQE TLASSTSTYK GITLFSTNWN VLQVRSGLGA VMFD S

UniProtKB: Capsid protein

Macromolecule #6: P1v1

• Macromolecule: Name: P1v1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 57.555555 KDa

Sequence

String:

MDDIETIEKY GRDETYIFLA DSAKRDTAAY PTAAEYEVLF NAQFRNVTKF ELLEVNIPRT EYLIDSSENT FAYALNQPTN INTWQQEIE GNIRIATITP GDYNLPQLID EMNNVLQQTA NTYGDSVILQ VSPVTNPSEI SNKIRITASG PFTLLGSTGT I GNTIGFGD PVNTSVASTT GYYSTVPGYS VNYPNGADYV FLSNQGNIGS EAVNEFVGPL PPGDNVSFTP IYTGQTPSQY FI APSAGVP TTVSAYFVDQ ATAPPGGFVV NYSIIKVSDS STIATGSLIS TNDDLVPSVS SPSVVSANFI QGQQYYIQFT PGS SGSSAG NCTALWYSFP NLPPVSGAYA AINGTLVFPG QYFCTDVSAG AYGNELTSPG IVNITGARYI KIRCKELEQL IYRD RVGEP TTAGIGIVNL IGYGFERSRY DFSSIPVKAF HPIGKLQKLT FRLERPNGTL YDTNGVDNTM LCALTFKVVP NNAVD KTFD GPGKYPAAPG YSGDYIQLQQ KRWGEEARAT YPTHKSTYNR CRPRTT

UniProtKB: DUF5901 domain-containing protein

Macromolecule #7: P2

• Macromolecule: Name: P2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 63.888082 KDa

Sequence

String:

MCNTYYKRVK FNLFLYTNSI EMELLAVASI IGYGLFSSQQ GRETRPDRNR YAEALGSGQG LDEDYDVKPT DMVRKYRKKA EKRWKKAQV PKESGIITPN MRPSEVMPYF TSGKSMNTNT DYKQRKMELF TGGVLDGHSV SGTYKHKVEA ANMFGMTPQG R VTSDGTVG NAPGDTELLK ARSVNSHQYN NVLPTEQLRV GPGLGVGPEV AATGGFHQFY RQLPLNINEY KLTQLPGRLV PG GTTTGGK GEIQQIASVN HNPDALVLNY DDRPPEATPN GAILASTQYG KQPRGYAGLR PYEKNYEGIA EADVSALQAR YLD QTRGRP RTGDGDTEPI INPNGERDGT GSYVTENMCS MTLESQRGLV NRYITPPGVT GVVQQGGEMR PEFVPETTIR EQYE DIYYT GPAGTTVTPT EPMNVVELQP ESRHAKRAGQ DRAYTPGAGR VNNFAPAAQG AYGLKDHPTY NALQHVVSEP IEQTF LPAA QGDDDRFGTK SNVNNPWGNP ASLQIANNQL AANKFNRDVT NTVNLDYDAG QPMKQQNFQP KAWIPNNTDD MKMLPL WKR KQLQAQKNKQ QRK

UniProtKB: Minor capsid protein P2

Macromolecule #8: P3

• Macromolecule: Name: P3 / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 19.116688 KDa

Sequence

String:

MAMKTQRKEN VLFQNVKPRE IPLVDNPFST YPYKHVITET QPTQAKNQAI WGLVQMGLSG EAAAMYGDVV VQKTTRACRK SEGGFKDVN TELWGTSPYL GRGDGEVYNM PASNQLLRGF ESSLRGSRVR TQIDDKSFIP YTWQMIDVPL AAAKTSFIAG L DTRQQLAY GNP

UniProtKB: Minor capsid protein 3

Macromolecule #9: P4

• Macromolecule: Name: P4 / type: protein_or_peptide / ID: 9 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 20.637311 KDa

Sequence

String:

MFSAFRDTAS IGFSDTHQDE KTLRFLKKQI SQFIKHLKEY YPNNELTKKL VMKYSDVQLL PYTKGATKDT YTSGLFDHTT GVIKIAPRD GLGNVRDEQS LNKSICHELA HGTRVKYPGE SSHSDEWKDA WKTFLKIAAD ELGWKIEVPC SSVSFYGLTK D DCENCVWD QDPETCPKTA KLA

UniProtKB: Minor capsid protein P4

Macromolecule #10: P5

• Macromolecule: Name: P5 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 16.455834 KDa

Sequence

String:

MDSRLSAAYA IRAARISMIP GGVDGLVINY AEGGEPAWVQ YPLKKQKPLP NNLCYTPTLE DIARKREAVI AKYTKQPLET GTTFTHVLN ASHLNEQYTR VKKSALPDKE FPIIETEKYP EPPILWETTI GAPSRLFDRS DGVKYVR

UniProtKB: Minor capsid protein P5

Macromolecule #11: P6

• Macromolecule: Name: P6 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 24.036729 KDa

Sequence

String:

MILVGIAVLI LLAVFAILYY KQKEKFVVVG KFVEPIPSNP GQDFTLLPMD QTYTFADPVP DTATAFDVVL SRFTDKKAPA DLLKGATFP EAAPYTDSEV ENISKLALSR VKGPDAPVLS FISVEYAAKG VDNKKNTHYD IAFMVYDQVK NFSLKLVLVA V LDAKNKLW IKKFSSFNSF TPKDKGPKGV ENIDETPLAE FIPDFVQFSR LYKDNANV

UniProtKB: Minor capsid protein P6

Macromolecule #12: P8

• Macromolecule: Name: P8 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 19.226947 KDa

Sequence

String:

METIGNFIQN MAFPTENPYK LSGDFGNSTL EPTVTAALRI LHESPAPFNT EFFSRKNVDF IQKKLISETK RYTSFDIGPQ NEDELIMMM AGIYVQDSTF DGNIKAGLRK LNTLVITECL KQILPGVRAY ALYVRDASLP FSGGGEEAFK RPELATLKGS K VLSGFLPL DRNAS

UniProtKB: Minor capsid protein P8

Macromolecule #13: P9

• Macromolecule: Name: P9 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 23.407564 KDa

Sequence

String:

MKTETLYQDP VWFQDLSVIF KRPSEIIPTR DQSDSERINA MVRLVLYCSF AVALIRQNYL YAILGLAIIA IISLAYALGA KKTKSNEAY GNIRPYSVKR SKKSCSKSSA NNPFSNATVG ALLDNEARPP ACSYDDNDMA STMRKNFNKG LFRNLDDVYE V ENSQRQFY TMPVTTAAPD LTAFGQFLYG SKGKTCKEDP SACTPAFATR DG

UniProtKB: Minor capsid protein P9

Macromolecule #14: P11

• Macromolecule: Name: P11 / type: protein_or_peptide / ID: 14 / Number of copies: 12 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 23.322656 KDa

Sequence

String:

MDMHMIVKVV AILAVLFLVY KLWESMNKPN ASPLKIQNPY EKYMNSAEGG EYDAEDDDIY YPETDAEDDD IYTGETDDMY DGEDDDIYV QEGDDIEDAE DEPYDDSADM EQDVPKVQQP MMPLLTPSSQ LLPKPSPEAA DFAQFAPKNL QAQNFLTATQ W IGVNTQGS SLKNANYDLR ADPIIPKADV GPWMMSSVDP NIYQKPLFG

UniProtKB: Minor capsid protein P11

Macromolecule #15: P12

• Macromolecule: Name: P12 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 17.715475 KDa

Sequence

String:

MGNGPPMERA VSSDDILTYY NTFIFFIYFN FTNENIYIIY TIYMKVQNTI VYIVLLLIVV VIIWNFTRKE GWSDYNAPND FMKIYYSNI VEDKKLAEKY PFFGTGPFTG LRCRKPNNVG CNTTWVSGQL VELTPKLKEQ IECKFGIQYV KT

UniProtKB: Minor capsid protein P12

Macromolecule #16: P13

• Macromolecule: Name: P13 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 11.07083 KDa

Sequence

String:

MHKITPFLIA AVVAVIVLAV WLFKKDNKKE TWFSRDLNYG KANSKIWNAT VAKGLKGIAN ENAEIRKMYP YLGYGDFTGA ICKGPNNQG CTYYANYTR

UniProtKB: Minor capsid protein P13

Macromolecule #17: P15

• Macromolecule: Name: P15 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 18.627422 KDa

Sequence

String:

MWLFFFALAV IYMIYKRDVF KKIAVNLKMN GVSIPFVDKY SKQYPTYTKN ALFHVTRFNN AYQKTFEYKN ISIDTINNLF SIRDDVLYN ISEIKLRLPN DLTQEKEINY MYEKTDQRLM EYITDVKSRF HINIYPGTMS SAFEARNYRA SNDIVF

UniProtKB: Uncharacterized protein

Macromolecule #18: P16

• Macromolecule: Name: P16 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 9.844584 KDa

Sequence

String:

MQGGLFGTIK LMIMLFSYFA AYQLGKMQER PQSQWPKAKA GQNKYMVGDW AAWKPIYMGV LGVAVLLTLL GPGGVGGGMG GMFGGGGGY GGYY

UniProtKB: Uncharacterized protein

Macromolecule #19: P17

• Macromolecule: Name: P17 / type: protein_or_peptide / ID: 19 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 9.12237 KDa

Sequence

String:

MGAFTSFVLM LLFTGIILIA TNELTYNRPR EIQYRYLPRD LDSFIRTQEM PSAIFSSMWD VDTRRGGDGG PNPPGIRQSN

UniProtKB: Uncharacterized protein

Macromolecule #20: P18

• Macromolecule: Name: P18 / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 16.497771 KDa

Sequence

String:

MTTITYDTDL LPPPELKVPS LDQALAPESV KNDDPFLDLS YFPVPKGFDN VGSLELNNLS TAEDVATLQN QLNKLAEEKH KRSTWKGLT FRIAVQDMWE ALTGIPTDIY QNSGRVSLKE LLTRDDRLRG LGLIFFLVAV VSIFFLAAG

UniProtKB: Uncharacterized protein

Macromolecule #21: P19

• Macromolecule: Name: P19 / type: protein_or_peptide / ID: 21 / Number of copies: 25 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 43.094387 KDa

Sequence

String:

MFLYYKMNEV LNVNNGSSIN VIKILKTPGP DIIRPGKTYK KKDVFTPKFF KNGNVMYTCN TFSLNVPVNN SIATIDFAEH VNGAVFKIE YNRVNFIAPS LYPISGLGTA VVFDLQKGEK ASQRKITEFG NKDIRIADEI SDIAADDHSV LITTKLMSES T PGELSRDV VLNGEIATGR INMNTGFVSD IIHTKKISII DDGIVDYYVK INVPAKYSHG IVEVVSGTFL NDIMIHLVRN KN KWALMDS KMYIVNNTNG FVIAKNPDTA MGVSLLEWPR GAVVFPPYYN FKKFKNVNKW SISQQIASCV NTSVKIPGGE YSW KIRLFF GPIWQVQESI NSVKTVPHGN DYMYLYKEEI VKYKYQRNTK RNFHEYDYDY KF

UniProtKB: Capsid protein

Macromolecule #22: P20

• Macromolecule: Name: P20 / type: protein_or_peptide / ID: 22 / Number of copies: 8 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 137.671312 KDa

Sequence

String:

MSGYSNPLND PIMIRTMIVY GNLSATYFTG NGAALTQQPI ASNVPPTLRA DAFGNVTSPA NVISGNITTI DVISAGNINT RYVFGDGST LSGISTGNSV VGVQKIDIIG NAVSSTISTG SLRTNVAFTN ITANISNISY LSGNTVSNII NASNLIANIV N ANVMSGDI TLNRIVATDT RTINLFGNVS TNSFTAYGNV TANILTATTL TANSLQIESV SGNSVQKMIV GNLIGNVLTA RT ATFDTAN IPTITSNVGI FTVANIRTIT GDVRANVLNV SNIVTRSIGT DVVSNNIIAT IGNVQSMIIG NLSANTLSVS NGT FQNFTT TVGLNVTTLS ASVSNALVLS FTTGNSSSTT TTNLDAYGNT QFLRISTETS GINILNANSV SVGNLTIVGN VTST SNNIS GQVTSNSSQV QNINTNVIYS GNVFTSRFIA ANANIRSLTA SIGQVNSLTI TSGNLTSLSF VNGNGNGVIA TNANI SNLN AVSMSGFAFD ANVIIGDITA NILSSGNLNA NVFEANMLTS GNVVSTNGDT GTINANSIVL NVISGGDTRI DRLIAN SVT TGDFYTTSTI TAGVIDCAQG KISGNSSSNA SLISNVISAN TASFVNTSVG YGNLVNAVVI GNIIANVVTS GDANAVF LN SNLTTSGSIF GNISNSASIV AEYSNIRTMN VGNINSTTFN AEYLYVGNIT VTGVSNTGYL ICRNATFSLN SNIQTLIT E NVTTSNAGSN IFTNVITTGN AFSQNINTIN ANVLGITSVF SNVITNISNI RTLILLSNVS LGNLTATSAN VTSNVSVGN LIGNIVASNA FFNTATIRNL AIFDVTGNIL VAQSNASISN LTTERILLSD ANIANLSTSN VSSNIAVVTG TCRIDAINSS NITFTNTAT VSAAVVNVLG NLTVSNVINV QNLTANVGNI WQAVSNIQSM TTANIFTNTM TIINSFTYSN ISSQRLIATN T LTANGVNL FSNIANLTVS GNANVGRWIA ASAPATGALC FSSTESANLT TANLFAGNLN TWRAFVGNVI GNVMTTVAGD FG GIRVSVA NIDVSGVANV ENFTVNGNLF ATNVITRDLS ANLINFSGSL SNTSSISISG NSLFTSSANA ANVGVSINMI TQN LFGNRL SSENIQGNVL QASNIAVSQT VNVVGNISIG NLSVSRELFA NSITISSGGT IVGNNTTRMI TTPTSNSWSV GSLV GNANV SVQFTANTMV VQNIQPNTLV VNINQSTPTS NSGVRAIYIG YIVPVNFNAT SSTTVSFSPA LPTNCIYMPQ LQYYS GGTV LQNNASFSTQ IGLGVETITN TSCTIRMSTL DTLPIPSTSF FGLMVTAVQT V

UniProtKB: Chlorovirus glycoprotein repeat domain-containing protein

Macromolecule #23: P21

• Macromolecule: Name: P21 / type: protein_or_peptide / ID: 23 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 141.414188 KDa

Sequence

String:

MSWFDPNWNP FFNRSIIVSG NLVVAGGVIE GNGGGLTNSA FSNPDTIRTD LTGNVTSNGT VRSSLIQTNS IVASGDAYAN VWNGNAAFI TGISANTTLV GNVRISISGN LTGNFAVSTT TVSNTMTANV LIGTTLTVNN LSATRANVQV LTGNVTGNVR L IANVVNVA AYTVGNLTTS SNVSTTNLNV TSNINGNVRS STANVQGRLS ATTPTTGSII SSSFIANSFT SSGNVQIGDF FG NVRASVG TFDMIASNVF SNVANIIEIR SDIISNIANV GNGTFVFVNA SNITTTNITG NITSNVASFS NVDSIFGNVG NLR ANTLTV TYANITGTLA SGNVAVGNLI SADNTSEFAN ITSFTTNGLV VNGNIIAAIG NGNVFLANVI TANSLTLQSS SSTA ASNVT TTRWIQSTTS TSNVMTIGNI TSGNVISSNA AYFANVISNT ITVMSAMTVS GNVSFGNVSF GNVSYGNITA NVTTS TGNV SVDNLTSNVV NVVFCNASSV TANTLTSIAL TGNTYVYSAN TGVLTANVGN VFGTLTVGVA NVTSMVSNAL FANTAV VSN LSVSNLTVTI SSDISNISIT GNTSGNVFAA NIATIGTLNT ANVVANLVAS NVMNAWVTSN IRTLITGNAN VSTTTSN VI TTGGFTITGN ITSGLLTSNV IAGNITMYNT SNTTLFTSNT SNIANFFAGN MTAVNTIVSN LEIQGNSVVI TQTTPFKV T SVLLANVLFA NTIISNTFTT TANVVGNIST DIANIGIANV NFLNTTDFAV NTANIVNYTP TSNINVTGNL TLGNANIVN FYATSANIVG NITANNAVIT FLTTPFYKGS GTVSAGFTSI ISANALSNVI VFGNLSANIV VSNTLLSNSI NVATVFSNVV NIGQVTSTG TTLVNSINFN ISNVDVSGNV LVTRDVYTTN ISVTTANIAN VTFFSNVAIG NLISTRNLTA ANLISSSDLF N SGPYTSSQ NVTIDTLNFT AGNLGTVAAR TTITTPTLFA TDVNFTQDAL VAGELITQNF YGNITSANIG SRITIGNANV TQ TNITGNV VIPRTSNAAG FNSRLLISNN TTVTSNIVAN SLISTGNIIT NLLQTTGQVS FASLAVEYID VANLAVRNVV TIG GNLTVS NVANLFSITA NTVNMSTVTT NTLSANTITG TSNVLVAGNI IGNCFGNVLV NRGVVTGNVF ADTITVPLNA VGVL TGNAL IVPNTALHSV AITGSSAFTS NIRTLNTPNA FIWNTSVPSS GLLDARRLRF SQYITSNRIV EMRYFYITNA LPQKY DSGG LNARYDLSFG TTLPTSQGQT WHHFLNTLYI GAQYNTNFSI NCLIINATTT GLEVIIYNPF GIAASLSSST PELYFY ITS IATSTQ

UniProtKB: Chlorovirus glycoprotein repeat domain-containing protein

Macromolecule #24: MCPv5

• Macromolecule: Name: MCPv5 / type: protein_or_peptide / ID: 24 / Number of copies: 3 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 45.585547 KDa

Sequence

String:

MGGIMQLVST GYQDVFLTGD PTRSLWKRIM ARKTNFAIES IETVFDVLYG STSFINIKKA GDLLKSCVLE ITMKRTSTES FYPAEQFIK SLTLLIGDQE VEKIQDFPTW SRVHDELFND TEMRSANYRM LNFRPDDPPG AIRTFYLDLP LFFTRYLSNS L PLVALQYH EVKLKIDFEP PYNIPGIDST YMPQVRFYGD YVFLDKPERV YFAQTEHEYI IEQLQTFVTI PNMSNSVNTT MV DLPFTLP SRYIIWVYKT NLHGQYTTSN STFVTNEGYA PLQSAVIKCN GTDRFSERPG GYFNMVQTTQ ALGQAPSCGI YMY SFGVNA DKQDPEGTLN FSKLDMVTLS YTNKAATAAD ISQVFDLSTT LENGITKFKN ITIFSKNFNV LRIVEGQGGI LFSN

UniProtKB: Capsid protein

Macromolecule #25: P22

• Macromolecule: Name: P22 / type: protein_or_peptide / ID: 25 / Number of copies: 3 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 137.927828 KDa

Sequence

String:

MGSYFVPPAN YFFKDIFASN VGNIANVIFD NGNVIAAGGL GYLIGNGAFI TGVTSTAIAN IPAVVTADIR GNLIGNYANV NNIIASSGN ISNVRFVSGG NVTASYYFGD GSQLTGITAT ANIPSIVTAD IRGNIIGNYA NVSNVSATFG NIANVLFNNG N VTAAGGNG FFIGNGSLLT GITATANIPS IVTADIRGNI IGNYANVSNV SATFGNIANV LFNNGNVTAA GGNGYFFGNG AL LTGITAT ANIPSIVTAD IRGNIIGNYA NVSNVSATFG NIANVLFNNG NVTAAGGNGY FFGNGALLTG ITATANIPSI VTA DIRGNI IGNYANVSNV SATFGNIANV LFNNGNVTAA GGNGFFIGNG SLLSGITATA NIPSIVTADI RGNIIGNYAN VSNV TATFG NIANVLFNNG NVTAAGGNGY FFGNGSQLTG VTATLPSIVT ADIRGNIIGN YANVSNVIAT FGNIANVLFN NGNVT AADG NGYFFGNGSQ LTGVTATLPS IVTADIRGNI IGNYANVSNV IATFGNIANV LFNNGNVTAA GGNGYFFGNG ALLTGI TAT ANIPSIVTAD IRGNIIGNYA NVSNVIATFG NIANVLFNNG NVTAADGNGY FFGNGSQLTG VTATLPSIVT ADIRGNI IG NYANVSNVIA TFGNIANVLF NNGNVTAAGG NGYFFGNGAL LTGITATANI PSIVTADIRG NIIGNYANVS NVTATFGN I ANVLFNNGNV TAAGGNGYFF GNGSQLTGVT ATLPSIVTAD IRGNIIGNYA NVSNVIATFG NIANVLFNNG NVTAAGGNG YFFGNGALLT GITATANIPS IVTADIRGNI IGNYANVSNV TATFGNIGNV LFNNGNVTAA GGNGYFFGNG TFLNFSTITA DIRGNIIGN YANVGNVIAG NVSTTLGNIG NVLFNNGNVT AAGGNGYFFG NGTSLTFSTI RADIRGNIIG NYANVANVIA G NVNSTFGN IAGVTFDAGN VSSPVDILVS GNVSVGSDGL FRGPTNQSNN ALILRGIGGT NTVNLFSIGA PSGQMRFSVP AS GVAFYNF LYGTNQVASL GPQGFYSLSY DSSVVVGQVV SNSTTYSGTI FKTEANRNSS TAFNHISCTG SNGNVFRVRG DGT TYGVGA FQTSGADYAE MMEWEDKNPT FEDRRGYPVV LSGNGKIRIA SLSDDYNNII GVVSSNPSML ADMAWDQWEG KYLK DKFGM RLSNTIYYLA NISNENEFTR VGPMTTPPQG YFIKTSPEYI LNPKYNPNVA YVERNDRPEW DPVGFVGKLR VRNGC LVHP SWKPLKVIDD YADVGNAAAQ VTEYLIGVTP NYTLSKKVED LEQTINVLKT QVQMLLGNI

UniProtKB: Peptidase G2 IMC autoproteolytic cleavage domain-containing protein

Macromolecule #26: P23

• Macromolecule: Name: P23 / type: protein_or_peptide / ID: 26 / Number of copies: 3 / Enantiomer: LEVO
• Source (natural): Organism: Paramecium bursaria Chlorella virus 1
• Molecular weight: Theoretical: 140.121688 KDa

Sequence

String:

MASGWSDFRA DPVIVNQDVV VFGNVFVDYL IGNASEMTGA ADFVPGNVVN VNIIGNTVST FVKSDVLMGD TITIDGNITA TRLYGDASN MSGLPTLPPN ANIDMVGNIV ANTNTNKFVS VDTFTGDVTT NVATISNANV GTVTTNTTFF GNVITNVFNI G NLILTSSN VDTLNVTSLV ASNVVSSQVD VQATIANSDL NVTRFDATSI SAEIFVSSET LAVSNITNLI ANIANIQGTT TV TGNLVGN IANVNTLTGN VTGNLFFTNL IIGNITANIF NTTTANVSNL ITSNVSASNV SASNVTSTLF TIGNLNTNVA TIS NLFVTG TTIAGNTTFS SFSVSSLVAN ISGNNASIPT FTPNVLSTSN ITIDGNAVVT GNAGFRTLNV TSLTANVLTT RGDV SNLYT DVINVNTNVF ISSANILANN VITVQMNNIS NVNITGNAEA FDVSANSVLM STLSVGGILS LGNVNTNDIS FGNIV TGNF FANFANVGNV QGNANVITMY STTLTSNSAQ IGNISGFSIV SNLGNAVSMF VGNLNTGTLV ANNSTVGNIT YISGNI GNA NAQTVRVSGL LSASGVALTF NSITSNVAGN SLTVHGNLRT NSVTTEILTG NVGNLSILNT GNLFANSISV GQSFVIS NF ANAFIISSQT TNASVITANI SGNIRVTNTL EANVVNSDSA NIIIKNVSTS GNVSNTFTTG NLTVTNAVFR SGITGNNI E VVGNVNCDGN TTVTTLSYGN LITSVYNTRN IFGNITANTV NITNSNIGNV VTSNINANSL IITNLIPTVD ITANVLRAS QVNTGWFYGN ATCNVLSMSN SVSINTLLSA EVFTSETINA NANVSVATIN SLGNTVAISR PSFLGNANIR LVISNVITIG NLTANTLVG DSFTATGIVN AINSNSQSDS IATNVTGNII IRGNLILASS ASAQSNASVF NPTNLISLNA NSLSSLTATN V SANNVVIS NTWQVSNLIV SNISAPNVTA NSFQAISMTG RYYRPGISIE RAGNLIVSNS LTSTANILQV LTSNTGQVNI TN TMFGNIS MSNIIVTGVV VTGNLTMGNV IANAVTTSVS TITGNATFGN LTVTDAVIIR GNITANNIST GSYIYGNGAF ITG NLTSSG NANISIATRM FGTNSAINVA GTFTGVGNTN TTNATIANLT TNTLLSIGNL STTGNFTVNS LSVGNLFANG STIQ LSNLA NIQVSNLIYS GNVVVSNLSA NTLSYVQNIG TSTQLQSGTM NVNNILSAGR FRLSISSTAP VFAGWTMGRV SLSGQ SLRT NSGNPRTITF TTPLPAGYSY GIQLSVYSTV FGQTMALFNI TVVSLTNTSV QFYIWNNPGG SGDSNTYIGY FAYAY

UniProtKB: Chlorovirus glycoprotein repeat domain-containing protein

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.8
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 24.4 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

Startup model

Type of model: EMDB MAP
EMDB ID:

5384

• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56500
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
• Final angle assignment: Type: PROJECTION MATCHING / Software - Name: jspr