6k32

RdRp complex

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

RNA-dependent RNA polymerase

Cypovirus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 7 RNA 2	Viral structural protein 4 × 1 （C7EWL9） ;RNA (5'-R(PUPUPAPCPU)-3') ; × 1 ;RNA (5'-D((3PO))-R(APG)-3' ; × 1 VP1 × 1 （D3JWE6） VP1 × 3 （D3JWE6） VP1 × 1 （D3JWE6） MAGNESIUM ION × 2 7-METHYLGUANOSINE × 1 DIPHOSPHATE × 1 ;2'-O-methyladenosine 5'-(dihydrogen phosphate) ; × 1 ;URIDINE 5'-TRIPHOSPHATE ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D0EZK6_CPVBM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1208； UniProt 5–1212

Viral structural protein 4

Cypovirus 1

UniProt C7EWL9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 7 RNA 2	RNA-dependent RNA polymerase × 1 （D0EZK6） ;RNA (5'-R(PUPUPAPCPU)-3') ; × 1 ;RNA (5'-D((3PO))-R(APG)-3' ; × 1 VP1 × 1 （D3JWE6） VP1 × 3 （D3JWE6） VP1 × 1 （D3JWE6） MAGNESIUM ION × 2 7-METHYLGUANOSINE × 1 DIPHOSPHATE × 1 ;2'-O-methyladenosine 5'-(dihydrogen phosphate) ; × 1 ;URIDINE 5'-TRIPHOSPHATE ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C7EWL9_CPVBM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–559； UniProt 2–560

VP1

Cypovirus 1

UniProt D3JWE6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 7 RNA 2	RNA-dependent RNA polymerase × 1 （D0EZK6） Viral structural protein 4 × 1 （C7EWL9） ;RNA (5'-R(PUPUPAPCPU)-3') ; × 1 ;RNA (5'-D((3PO))-R(APG)-3' ; × 1 MAGNESIUM ION × 2 7-METHYLGUANOSINE × 1 DIPHOSPHATE × 1 ;2'-O-methyladenosine 5'-(dihydrogen phosphate) ; × 1 ;URIDINE 5'-TRIPHOSPHATE ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D3JWE6_CPVBM
Isoform	—
PDB entities	5, 6, 7
Chains and sequence ranges	Author chain C； PDBConstruct 1–1220； UniProt 114–1333 Author chain D； PDBConstruct 1–1205； UniProt 129–1333 Author chain E； PDBConstruct 1–1205； UniProt 129–1333 Author chain F； PDBConstruct 1–1205； UniProt 129–1333 Author chain G； PDBConstruct 1–1226； UniProt 108–1333

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6k32
Deposition date deposition_date	2019-05-16
Structure title title	RdRp complex
Keywords keywords	Cypovirus, Transcription, RNA-dependent RNA polymerase, VIRAL PROTEIN-RNA complex; VIRAL PROTEIN/RNA
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6k32__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6k32__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6k32__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	82.13 Å
Rg (electron density)	81.99 Å
Total Rg	81.93 Å
Atom count	61364
Residues	7730
Excluded volume	1089300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6k32__assembly_1__model_1`	nonameric （9）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Description description	RNA-dependent RNA polymerase
Molecular weight formula_weight	137058.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	61364

TKLHNTIFSETRKFTRESFKEIEHLTARLANDRVARHDFLFNTSIVLISDYSGEDSNGNQLQATITIPNEIINPKEYDPSDYPLAEDESFFKQGHKYDYLVTFRAGSLTNTYEPKTKMYKLHAALDKLMHVKQRKSRFADLWRELCAVIASLDVWYQTTNYPLRTYVKLLFHKGDEFPFYESPSQDRIIFNDKSVASILPTFVYTCCQVGTAIMSGILTHVESIVAMNHFLHCAKDSYIDEKLKIKGIGRSWYQEALHNVCQATVPVWSQFNEVIGHRTKSTSEPHFVSSTFISLRAKRAELLYPEFNAYINRAIQLSKTQNDVANYYAACRAMTNDGTFLATLTELSLDAAVFPRIEQHLVTRPAVLMSNTRHESLKQKYTNGVGSIAQSYLSSFTDEIAKRVNGRHHDEAWLNFLTTSSPGRKLTEIEKLEVGGDVAAWSNSRIVMQAVFAREYRTPERIFKSLKAPIKLVERQQSDRRQRAISGLDNDRLFLSFMPYTIGKQIYELNDNAAQGKQAGNAFDIGEMLYWTSQRNVLLSSIDVAGMDASVTTNTKDIYNTFVLDVASKCTVPRFGPYYAKNMEVFEAGNRQSQVRYVNAAWQACALEAANSQTSTSYESEIFGQVKNAEGTYPSGRADTSTHHTVLLQGLVRGNELKRASDGKNSCLATIKILGDDIMEIFQGSESDTYDHAVSNASILNESGFATTAELSQNSIVLLQQLVVNGTFWGFADRISLWTREDTKDIGRLNLAMMELNALIDDLVFRVRRPEGLKMLGFFCGAICLRRFTLSVDNKLYDSTYNNLSKYMTLTKYDKNPDSDSTLMSLILPLAWLFMPRGGEYPAYPFERRDGTFTEDESMFTARGAYKRRLLYDVSNIGEMIQQNSMALDDDLLHEYGFTGALLLIDLNILDLIDEVKKEDISPVKVSELATSLEQLGKLGEREKSRRAASDLKIRGHALSNDIVYGYGLQEKIQKSAMATKETTVQSKRVSSRLHDVIVAKTRDYKISTIPADALHLHEFEVEDVTVDLLPHAKHTSYSSLAYNMSFGSDGWFAFALLGGLDRSANLLRLDVASIRGNYHKFSYDDPVFKQGYKIYKSDATLLNDFFTAISAGPKEQGILLRAFAYYSLYGNVEYHYVLSPRQLFFLSDNPVSAERLVRIPPKYYVSTQCRALYNIFSYLHILRSIANNRGKRLKMVLHPGLIAYVRG

Source Source

Source organism organism	Cypovirus 1
NCBI taxonomy ID ncbi_taxonomy_id	205895
Host organism host_organism	invertebrate environmental sample

Entity 2 Entity 2 polymer

Description description	Viral structural protein 4
Molecular weight formula_weight	63379.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

FAIDPLKHSKLYEEYGLYLRPHQINQEIKPTTIKKKELAPTIRSIKYASLIHSMLAEHAARHNGTLINPRMYADMITLGNTKVTVTKGTPKAQIDTLKMNGLTVVSKSRRNNKKKPVSDTTATIDENTNAIVTYKALTEMSTLIESFRLPSGLTLIIFDDEKYQSLIPNYINQLIAYTQPHIIPTWQGIADFSDTYLRSYFKRPFELTASNLAAPQKHNLSPMTRSIFNNTGREDAVIRKLYGYGEYVFIKYEGCLITWTGIYGEVTMMVNLSKRDLGLDVGDDYLKEYKKLLFYGVITDAIPSGISTRSTIMKISPHKMMNPSGGALAVLSKFLEAVVSTNVINATLVVYAEKGAGKTSFLSTYAEQLSLASGQVVGHLSSDAYGRWLAKTKDIEEPSFAYDYVLSLDTDDNESYYEQKASELLMSHGISEVAQYELLSVRKKIKMMDEMNEVLIAQLENADTHSERNFYYMVSTGKTTPRILIVEGHFNAQDATIARTDTTVLLRTINDTTQAMRDRQRGGVVQLFLRDTYYRLLPALHTTVYPFEMLESIKRWKWV

Source Source

Source organism organism	Cypovirus 1
NCBI taxonomy ID ncbi_taxonomy_id	205895
Host organism host_organism	invertebrate environmental sample

Entity 3 Entity 3 polymer

Description description	;RNA (5'-R(PUPUPAPCP*U)-3') ;
Molecular weight formula_weight	1507.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	t

UUACU

Source Source

Source organism organism	Cypovirus 1
NCBI taxonomy ID ncbi_taxonomy_id	205895
Host organism host_organism	invertebrate environmental sample

Entity 4 Entity 4 polymer

Description description	;RNA (5'-D((3PO))-R(AP*G)-3' ;
Molecular weight formula_weight	869.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	p

XAG

Source Source

Source organism organism	Cypovirus 1
NCBI taxonomy ID ncbi_taxonomy_id	205895
Host organism host_organism	invertebrate environmental sample

Entity 5 Entity 5 polymer

Description description	VP1
Molecular weight formula_weight	136769.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

VQSRTDVFNEQFANEALHPMTKVIFNGLDVNTEVQPLSDDFKQISDPKGYLTYSVKYEDQFTKKDKLRASEADDRIVGPTVNLFKYGAAVVNIDLNRDFFDTATGIDLTKGIPLVQDLLVPIGVTAGAEQSAEYVSGLLMVLFKVMTDNRLVIVGETTTPMSNTLSTVVNNVLRTTYHNNVGVNPALLRDFTQVNWLNRDITNMLQQAGTKYGLGLTETRLDYVRLVKTIVGHALNIDHFAASVLNINLRALMEANVTADDRIKALQAHSMISTQFHGPNQGALRPELAFDHDHIIRCLMLAAANYPRLEGIIVQINTGYVASANVIRPVSEKRYFPENLEQNQSAARLVSAVKARASEADISSIHLAIAREVSPMFNVHELKKIAESFEDPSSIVVVLEFILFALFFPTEFNRIKGDIQNVLLLFFSRWYPVEYGIFIQRGATYTINAAGEFEFSGRNEKWDQSLYLSEHFPALFSDVPLAGANTIIAIMRLFTPQGFLRTDDLAIAANFPRASRNPQTYIPYTNQRGTVTNEFASRFRTIVATLANVVNERAVQDDMQKATRSCTKQWLRHLETQFDNIAVAHTDHLSVVYATMSNFMLNFTNNFSGNHATFKPDQYVITSPEGSYKPIIERQGETVDGLTIIDTSIVWPILCQCTYPLVRQSGKGVDAVSIMEEIVYPDPSTTLSQSLSVAQVLSKLTLPDAFINMILSGGDSVVMRTYQTEADDDLDEGIRMTTYDQYLSHIRERLHITNVPDPIYITGASTPDQIAASVQATHVAVVLYQSGVINGSASTYLRENEVLVVMPDYYDVVSRFANANLQMNNNRYHESVLEIADIFDQADFIQTSDAVRQLRALMPTLSTSQIRHAIERIAQITDVDSTDYGKLTLRFLGTLTRSLKMQNAQIRRIRPDGTVLRYDDQIDIEAFRWSRYFLDELRLRRLSVGLRLITNPRIARRFDGVRIMYLTDDDPDPDFVPDVPEGYVAVQYAHRLFSSSLANKRNRVTYTHPPTGMAYPSPTGRPHVHMTINERAGMSKLVADNIIASVIKSNWVVDIHDIEYTAEVMTPSEGYTQHVDAESIMTAPKGKLFHLQFMDGLLRPEPSAFDPPASGEDMRLIYPLQPISVARSMRAIVNHNEVDRPRGAVAPSSYEMDTGTLSRNGDLLYSPVANGQVGIPKLEVDHISFSNVVSMMTANIRTGDDMAVERVNPDDVRAINIRNA

Source Source

Source organism organism	Cypovirus 1
NCBI taxonomy ID ncbi_taxonomy_id	205895
Host organism host_organism	invertebrate environmental sample

Entity 6 Entity 6 polymer

Description description	VP1
Molecular weight formula_weight	135002.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

ALHPMTKVIFNGLDVNTEVQPLSDDFKQISDPKGYLTYSVKYEDQFTKKDKLRASEADDRIVGPTVNLFKYGAAVVNIDLNRDFFDTATGIDLTKGIPLVQDLLVPIGVTAGAEQSAEYVSGLLMVLFKVMTDNRLVIVGETTTPMSNTLSTVVNNVLRTTYHNNVGVNPALLRDFTQVNWLNRDITNMLQQAGTKYGLGLTETRLDYVRLVKTIVGHALNIDHFAASVLNINLRALMEANVTADDRIKALQAHSMISTQFHGPNQGALRPELAFDHDHIIRCLMLAAANYPRLEGIIVQINTGYVASANVIRPVSEKRYFPENLEQNQSAARLVSAVKARASEADISSIHLAIAREVSPMFNVHELKKIAESFEDPSSIVVVLEFILFALFFPTEFNRIKGDIQNVLLLFFSRWYPVEYGIFIQRGATYTINAAGEFEFSGRNEKWDQSLYLSEHFPALFSDVPLAGANTIIAIMRLFTPQGFLRTDDLAIAANFPRASRNPQTYIPYTNQRGTVTNEFASRFRTIVATLANVVNERAVQDDMQKATRSCTKQWLRHLETQFDNIAVAHTDHLSVVYATMSNFMLNFTNNFSGNHATFKPDQYVITSPEGSYKPIIERQGETVDGLTIIDTSIVWPILCQCTYPLVRQSGKGVDAVSIMEEIVYPDPSTTLSQSLSVAQVLSKLTLPDAFINMILSGGDSVVMRTYQTEADDDLDEGIRMTTYDQYLSHIRERLHITNVPDPIYITGASTPDQIAASVQATHVAVVLYQSGVINGSASTYLRENEVLVVMPDYYDVVSRFANANLQMNNNRYHESVLEIADIFDQADFIQTSDAVRQLRALMPTLSTSQIRHAIERIAQITDVDSTDYGKLTLRFLGTLTRSLKMQNAQIRRIRPDGTVLRYDDQIDIEAFRWSRYFLDELRLRRLSVGLRLITNPRIARRFDGVRIMYLTDDDPDPDFVPDVPEGYVAVQYAHRLFSSSLANKRNRVTYTHPPTGMAYPSPTGRPHVHMTINERAGMSKLVADNIIASVIKSNWVVDIHDIEYTAEVMTPSEGYTQHVDAESIMTAPKGKLFHLQFMDGLLRPEPSAFDPPASGEDMRLIYPLQPISVARSMRAIVNHNEVDRPRGAVAPSSYEMDTGTLSRNGDLLYSPVANGQVGIPKLEVDHISFSNVVSMMTANIRTGDDMAVERVNPDDVRAINIRNA

Source Source

Source organism organism	Cypovirus 1
NCBI taxonomy ID ncbi_taxonomy_id	205895
Host organism host_organism	invertebrate environmental sample

Entity 7 Entity 7 polymer

Description description	VP1
Molecular weight formula_weight	137422.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

KKPPTVVQSRTDVFNEQFANEALHPMTKVIFNGLDVNTEVQPLSDDFKQISDPKGYLTYSVKYEDQFTKKDKLRASEADDRIVGPTVNLFKYGAAVVNIDLNRDFFDTATGIDLTKGIPLVQDLLVPIGVTAGAEQSAEYVSGLLMVLFKVMTDNRLVIVGETTTPMSNTLSTVVNNVLRTTYHNNVGVNPALLRDFTQVNWLNRDITNMLQQAGTKYGLGLTETRLDYVRLVKTIVGHALNIDHFAASVLNINLRALMEANVTADDRIKALQAHSMISTQFHGPNQGALRPELAFDHDHIIRCLMLAAANYPRLEGIIVQINTGYVASANVIRPVSEKRYFPENLEQNQSAARLVSAVKARASEADISSIHLAIAREVSPMFNVHELKKIAESFEDPSSIVVVLEFILFALFFPTEFNRIKGDIQNVLLLFFSRWYPVEYGIFIQRGATYTINAAGEFEFSGRNEKWDQSLYLSEHFPALFSDVPLAGANTIIAIMRLFTPQGFLRTDDLAIAANFPRASRNPQTYIPYTNQRGTVTNEFASRFRTIVATLANVVNERAVQDDMQKATRSCTKQWLRHLETQFDNIAVAHTDHLSVVYATMSNFMLNFTNNFSGNHATFKPDQYVITSPEGSYKPIIERQGETVDGLTIIDTSIVWPILCQCTYPLVRQSGKGVDAVSIMEEIVYPDPSTTLSQSLSVAQVLSKLTLPDAFINMILSGGDSVVMRTYQTEADDDLDEGIRMTTYDQYLSHIRERLHITNVPDPIYITGASTPDQIAASVQATHVAVVLYQSGVINGSASTYLRENEVLVVMPDYYDVVSRFANANLQMNNNRYHESVLEIADIFDQADFIQTSDAVRQLRALMPTLSTSQIRHAIERIAQITDVDSTDYGKLTLRFLGTLTRSLKMQNAQIRRIRPDGTVLRYDDQIDIEAFRWSRYFLDELRLRRLSVGLRLITNPRIARRFDGVRIMYLTDDDPDPDFVPDVPEGYVAVQYAHRLFSSSLANKRNRVTYTHPPTGMAYPSPTGRPHVHMTINERAGMSKLVADNIIASVIKSNWVVDIHDIEYTAEVMTPSEGYTQHVDAESIMTAPKGKLFHLQFMDGLLRPEPSAFDPPASGEDMRLIYPLQPISVARSMRAIVNHNEVDRPRGAVAPSSYEMDTGTLSRNGDLLYSPVANGQVGIPKLEVDHISFSNVVSMMTANIRTGDDMAVERVNPDDVRAINIRNA

Source Source

Source organism organism	Cypovirus 1
NCBI taxonomy ID ncbi_taxonomy_id	205895
Host organism host_organism	invertebrate environmental sample

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	7-METHYLGUANOSINE
Molecular weight formula_weight	298.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	DIPHOSPHATE
Molecular weight formula_weight	173.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	;2'-O-methyladenosine 5'-(dihydrogen phosphate) ;
Molecular weight formula_weight	361.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 non-polymer

Description description	;URIDINE 5'-TRIPHOSPHATE ;
Molecular weight formula_weight	484.1 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	100000

RdRp complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

RNA-dependent RNA polymerase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Viral structural protein 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

VP1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6k32__assembly_1__model_1

6k32__assembly_1__model_1 | I(q)

6k32__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

7. Citations (1)