SAXSdb — 8qca

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

Antiviral helicase SKI2

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 5 RNA 1	Superkiller protein 3 × 1 （P17883） Antiviral protein SKI8 × 2 （Q02793） Superkiller protein 7 × 1 （Q08491） ;RNA (5'-R(PUPUPUPU)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SKI2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1287； UniProt 1–1287

Superkiller protein 3

Saccharomyces cerevisiae

UniProt P17883

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 5 RNA 1	Antiviral helicase SKI2 × 1 （P35207） Antiviral protein SKI8 × 2 （Q02793） Superkiller protein 7 × 1 （Q08491） ;RNA (5'-R(PUPUPUPU)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SKI3_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–1436； UniProt 1–1432

Antiviral protein SKI8

Saccharomyces cerevisiae

UniProt Q02793

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 5 RNA 1	Antiviral helicase SKI2 × 1 （P35207） Superkiller protein 3 × 1 （P17883） Superkiller protein 7 × 1 （Q08491） ;RNA (5'-R(PUPUPUPU)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SKI8_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–397； UniProt 1–397 Author chain D； PDBConstruct 1–397； UniProt 1–397

Superkiller protein 7

Saccharomyces cerevisiae

UniProt Q08491

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 5 RNA 1	Antiviral helicase SKI2 × 1 （P35207） Superkiller protein 3 × 1 （P17883） Antiviral protein SKI8 × 2 （Q02793） ;RNA (5'-R(PUPUPUPU)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SKI7_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 5–239； UniProt 1–235

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	8qca
Deposition date deposition_date	2023-08-25
Structure title title	CryoEM structure of a S. Cerevisiae Ski2387 complex in the closed state bound to RNA
Keywords keywords	Helicase, RNA binding, RNA degradation, HYDROLASE; HYDROLASE
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.

8qca__assembly_1__model_1

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

Download this curve (.dat)

8qca__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8qca__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.41 Å
Rg (electron density)	41.83 Å
Total Rg	42.01 Å
Atom count	17573
Residues	2330
Excluded volume	309740 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8qca__assembly_1__model_1`	hexameric （6）	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 (5)

Entity 1 Entity 1 polymer

Description description	Antiviral helicase SKI2
Molecular weight formula_weight	146259.1 kDa
EC 编号 ec_number	3.6.4.13
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	17573

MSEGFSSSSIQELYQSLKEITNNADVELFEDRITKLDFESTDEPKHANDIIKDRFLRPSNALPWSLLDMVQDVPHTSSPEDCSGKLDYKELLKVPDPINRTSYQFKRTGLEGKISGYKEEVDLKEVANANASNSLSITRSINHNQNSVRGSTAQLPFTPGGIPMKSVKTDSEQNGSSTMANATKLLHKDGQGLFDIPEGMNRGIKPMDSPAENEDQNGQFKELKQLNEIDNELDIRIEANEAKLKEEEKSAKSISEEIMEEATEETTADNADDAEIDELLPIGIDFGRTKPVSKSVPVKKEWAHVVDLNHKIENFDELIPNPARSWPFELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRDFKETFDDVNIGLITGDVQINPDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQDRGVVWEEVIIMLPQHVKFILLSATVPNTYEFANWIGRTKQKNIYVISTPKRPVPLEINIWAKKELIPVINQNSEFLEANFRKHKEILNGESAKGAPSKTDNGRGGSTARGGRGGSNTRDGRGGRGNSTRGGANRGGSRGAGAIGSNKRKFFTQDGPSKKTWPEIVNYLRKRELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPTRTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMAYNSPLSIATFKEVTMGVPTRLQSQFRLTYNMILNLLRIEALRVEEMIKYSFSENAKETLQPEHEKQIKVLQEELQTIEYKSCEICDNDIEKFLELMLAYKEATVNLMQEMVKSPSILHILKEGRLVAFRDPNDCLKLGFVFKVSLKDAVCVIMTFTKPYKLPNGEPNHLIYFPKADGYRRRNFPKFQKTDFYMEEVPVTAIEVITKRKFAAPLGKVIKKDVAALNEFNAETNNILDGKTLKEAINIEKQGLKIHQILLDRTNIRDEIFKLKSIKCPNLSQHIVPKFKAHVIKKKIEELYHLMSDQNLSLLPDYEKRLAVLKDTEFIDQNHNVLLKGRVACEINSGYELVLTELILDNFLGSFEPEEIVALLSVFVYEGKTREEEPPIVTPRLAKGKQRIEEIYKKMLCVFNTHQIPLTQDEAEFLDRKRFAMMNVVYEWARGLSFKEIMEMSPEAEGTVVRVITWLDEICREVKTASIIIGNSTLHMKMSRAQELIKRDIVFAASLYL

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Superkiller protein 3
Molecular weight formula_weight	164278.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPDSMSDIKQLLKEAKQELTNRDYEETIEISEKVLKLDPDNYFAHIFLGKALSSLPASNNVSSNRNLERATNHYVSAAKLVPDNLLAWKGLFLLFRTTEVVPDILSYDEYFDLCGQYADALLKQEQSQVELINDIKLLKKTHPDCQKAFYQHLKPGSLMAETIGRHLSTPQDALLNLIKILSNIETTEIGKTLSQNRLKLKASDPDYQIKLNSFSWEIIKNSEIDQLYNQLVNILADDQKRSEIENQWLEYRIKVLKSMPLDVKKDFFTKVKEMVEDMVLVNHQSLLAWQKYFEWTDYEDLDNMDAPLIIKYFKKFPKDPLAMILYSWLSSKLSKYDIKSLESANKPPEGHKKTEKETDIKDVDETNEDEVKDRVEDEVKDRVEDEVKDQDEEAKEDEEEDLDDIEIGLLEEEVVTVLTENIVKCKNNILAHRILCQYYLLTKEYEAALPYIKNGISLIAYNIKDLGVHLPLTKREFSLDLATVYTYVDAPKDHNAALKLYDNILSGDFSNIQAKMGKGIIFIERKNWKDAMTLLTQVHEQSPNNLEVLSELSWSKAHMGYMDEALAGLDTVIKGIKGMDLRSIDFRALNLWRQAKVYIMKHASINDAKQENVKCAFKLLIQSIKILDTFAPGFSTLGDIYCHYYKDHLRAFKCYFKAFDLDAGDYTAAKYITETYASKPNWQAASSIASRLIKGEKAKAELRSNNWPFRVVGIAHLEKQEESDSIEWFQSALRVDPNDVESWVGLGQAYHACGRIEASIKVFDKAIQLRPSHTFAQYFKAISLCDVGEYLESLDILEKVCQEAATEESFQIGLVEVLMRCSLDLYSQGFLLKSVSIAKDTIERIKIIISELKCENQQVWIYLSQVLRLFIWIESKVDTLPVESLVSIFENSQFSGSEEIDSVDNIKIDTLLDSTTDDNVSIACKFLILASKYSVSDQKFTDIAGTVRASYWYNIGISELTAFITLKEPQYRDAAIFAFKKSIQLQSNTSETWIGLGIATMDINFRVSQHCFIKATALEPKATNTWFNLAMLGLKKKDTEFAQQVLNKLQSLAPQDSSPWLGMALILEEQGDIIGSSKLFAHSFILSNGRSKAAQFMYAKNVLENHINNGDDERDIETVEKLTTASIALEQFFKKSPDSQFALQCALLTLERLHHYENANELANRLIGILEKKFEKTQDERELFNFAIIKGQFARIHLGLGNFELSIENADLSQGIISESSDEKSMKTKISNHICLGLSYFFLNDFDQTLNQFQELLSISKDSKHLVVLIAKVLYDVGESDTKEIALQELTEYIATSGADLLVTLTIAAMSILDDKREDLSIILEELKALPLSKQIIDKHKDAPYLIEEITKRLYRNDTGKQVWQRSAYFFPNNLKVWERLDKNIQRRIASNGQNKVTAEEMSKLYCESKNLRSIQRGMFLCPWNVTAVKALNECF

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Antiviral protein SKI8
Molecular weight formula_weight	44283.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MSKVFIATANAGKAHDADIFSVSACNSFTVSCSGDGYLKVWDNKLLDNENPKDKSYSHFVHKSGLHHVDVLQAIERDAFELCLVATTSFSGDLLFYRITREDETKKVIFEKLDLLDSDMKKHSFWALKWGASNDRLLSHRLVATDVKGTTYIWKFHPFADESNSLTLNWSPTLELQGTVESPMTPSQFATSVDISERGLIATGFNNGTVQISELSTLRPLYNFESQHSMINNSNSIRSVKFSPQGSLLAIAHDSNSFGCITLYETEFGERIGSLSVPTHSSQASLGEFAHSSWVMSLSFNDSGETLCSAGWDGKLRFWDVKTKERITTLNMHCDDIEIEEDILAVDEHGDSLAEPGVFDVKFLKKGWRSGMGADLNESLCCVCLDRSIRWFREAGGK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 4 Entity 4 polymer

Description description	Superkiller protein 7
Molecular weight formula_weight	28345.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GPDSMSLLEQLARKRIEKSKGLLSADQSHSTSKSASLLERLHKNRETKDNNAETKRKDLKTLLAKDKVKRSDFTPNQHSVSLSLKLSALKKSNSDLEKQGKSVTLDSKENELPTKRKSPDDKLNLEESWKAIKEMNHYCFLKNDPCINQTDDFAFTNFIIKDKKNSLSTSIPLSSQNSSFLSLKKHNNELLGIFVPCNLPKTTRKVAIENFNRPSPDDIIQSAQLNAFNEKLENLNIKSAGSWSHPQFEK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	;RNA (5'-R(PUPUPUPU)-3') ;
Molecular weight formula_weight	9140.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	X

UUUUUUUUUUUUUUUUUUUUUUUUUUUUUU

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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	2.84 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	371916

CryoEM structure of a S. Cerevisiae Ski2387 complex in the closed state bound to RNA

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

Antiviral helicase SKI2

State in the Current Structure

Other States of the Same Protein in the Database

Superkiller protein 3

State in the Current Structure

Other States of the Same Protein in the Database

Antiviral protein SKI8

State in the Current Structure

Other States of the Same Protein in the Database

Superkiller protein 7

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8qca__assembly_1__model_1

8qca__assembly_1__model_1 | I(q)

8qca__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

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

7. Citations (1)

CryoEM structure of a S. Cerevisiae Ski2387 complex in the closed state bound to RNA

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

Antiviral helicase SKI2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Superkiller protein 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Antiviral protein SKI8

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Superkiller protein 7

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

8qca__assembly_1__model_1

8qca__assembly_1__model_1 | I(q)

8qca__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

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

7. Citations (1)