SAXSdb — 7y38

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

mRNA-capping enzyme nsP1,affinity-tag (strepII-3XFLAG)

Chikungunya virus strain S27-African prototype

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 14 RNA 1	RNA-directed RNA polymerase nsP4 × 1 ;RNA (5'-R(PCPCP*A)-3') ; × 1 ZINC ION × 12 ADENOSINE-5'-TRIPHOSPHATE × 12 GUANOSINE-5'-TRIPHOSPHATE × 12	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLN_CHIKS
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–516； UniProt 1–516 Author chain A； PDBConstruct 553–570； UniProt 517–534 Author chain B； PDBConstruct 1–516； UniProt 1–516 Author chain B； PDBConstruct 553–570； UniProt 517–534 Author chain C； PDBConstruct 1–516； UniProt 1–516 Author chain C； PDBConstruct 553–570； UniProt 517–534 Author chain D； PDBConstruct 1–516； UniProt 1–516 Author chain D； PDBConstruct 553–570； UniProt 517–534 Author chain E； PDBConstruct 1–516； UniProt 1–516 Author chain E； PDBConstruct 553–570； UniProt 517–534 Author chain F； PDBConstruct 1–516； UniProt 1–516 Author chain F； PDBConstruct 553–570； UniProt 517–534 Author chain G； PDBConstruct 1–516； UniProt 1–516 Author chain G； PDBConstruct 553–570； UniProt 517–534 Author chain H； PDBConstruct 1–516； UniProt 1–516 Author chain H； PDBConstruct 553–570； UniProt 517–534 Author chain I； PDBConstruct 1–516； UniProt 1–516 Author chain I； PDBConstruct 553–570； UniProt 517–534 Author chain J； PDBConstruct 1–516； UniProt 1–516 Author chain J； PDBConstruct 553–570； UniProt 517–534 Author chain K； PDBConstruct 1–516； UniProt 1–516 Author chain K； PDBConstruct 553–570； UniProt 517–534 Author chain L； PDBConstruct 1–516； UniProt 1–516 Author chain L； PDBConstruct 553–570； UniProt 517–534 Author chain Y； PDBConstruct 1–798； UniProt 536–1333

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	7y38
Deposition date deposition_date	2022-06-10
Structure title title	Molecular architecture of the chikungunya virus replication complex
Keywords keywords	;replicase, replication complex, viral RNA replication, capping, helicase, protease, RNA-dependent RNA polymerase, RdRp, VIRAL PROTEIN, 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.

7y38__assembly_1__model_1

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

Download this curve (.dat)

7y38__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7y38__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	68.74 Å
Rg (electron density)	68.60 Å
Total Rg	68.77 Å
Atom count	53063
Residues	6707
Excluded volume	943120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7y38__assembly_1__model_1`	pentadecameric （15）	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 (7)

Entity 1 Entity 1 polymer

Description description	mRNA-capping enzyme nsP1,affinity-tag (strepII-3XFLAG)
Molecular weight formula_weight	64328.9 kDa
EC 编号 ec_number	2.1.1.-,2.7.7.-,2.1.1.-,2.7.7.-
Mutation mutation	H37A
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	53135

MDPVYVDIDADSAFLKALQRAYPMFEVEPRQVTPNDAANARAFSHLAIKLIEQEIDPDSTILDIGSAPARRMMSDRKYHCVCPMRSAEDPERLANYARKLASAAGKVLDRNISGKIGDLQAVMAVPDTETPTFCLHTDVSCRQRADVAIYQDVYAVHAPTSLYHQAIKGVRLAYWVGFDTTPFMYNAMAGAYPSYSTNWADEQVLKAKNIGLCSTDLTEGRRGKLSIMRGKKLEPCDRVLFSVGSTLYPESRKLLKSWHLPSVFHLKGKLSFTCRCDTVVSCEGYVVKRITMSPGLYGKTTGYAVTHHADGFLMCKTTDTVDGERVSFSVCTYVPATICDQMTGILATEVTPEDAQKLLVGLNQRIVVNGRTQRNTNTMKNYMIPVVAQAFSKWAKECRKDMEDEKLLGVRERTLTCCCLWAFKKQKTHTVYKRPDTQSIQKVQAEFDSFVVPSLWSSGLSIPLRTRIKWLLSKVPKTDLTPYSGDAQEARDAEKEAEEEREAELTLEALPPLQAAGGGGSWSHPQFEKMDYKDHDGDYKDHDIDYKDDDDKQEDVQVEIDVEQLEDRAGNGL

Source Source

Source organism organism	Chikungunya virus strain S27-African prototype
NCBI taxonomy ID ncbi_taxonomy_id	371094
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	RNA-directed RNA polymerase nsP4
Molecular weight formula_weight	68373.3 kDa
EC 编号 ec_number	2.7.7.19,2.7.7.48
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

YIFSSDTGQGHLQQKSVRQTTLPVNIVEEVHEEKCYPPKLDEIKEQLLLKRLQESASTANRSRYQSRKVENMKAMIIHRLKEGCRLYLASDTPRVPSYRITYPAPIYSPSINIKLSNPETAVAVCNEFLARNYPTVASYQVTDEYDAYLDMVDGSESCLDRATFNPSKLRSYPKQHSYHAPTIRSAVPSPFQNTLQNVLAAATKRNCNVTQMRELPTMDSAAFNVECFKKYACNQEYWREFASSPIRVTTENLTTYVTKLKGPKAAALFAKTHNLLPLQEVPMDRFTMDMKRDVKVTPGTKHTEERPKVQVIQAAEPLATAYLCGIHRELVRRLNAVLLPNVHTLFDMSAEDFDAIIATHFKPGDAVLETDIASFDKSQDDSLALTAMMLLEDLGVDQPILDLIEAAFGEISSCHLPTGTRFKFGAMMKSGMFLTLFVNTLLNITIASRVLEERLTTSACAAFIGDDNIIHGVVSDALMAARCATWMNMEVKIIDAVVSVKAPYFCGGFILHDTVTGTACRVADPLKRLFKLGKPLAAGDEQDEDRRRALADEVTRWQRTGLVTELERAVYSRYEVQGITAVITSMATFASSKENFKKLRGPVVTLYGGPK

Source Source

Source organism organism	Onyong-nyong virus
NCBI taxonomy ID ncbi_taxonomy_id	2169701
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Protease nsP2
Molecular weight formula_weight	89599.8 kDa
EC 编号 ec_number	3.1.3.33,3.4.22.-,3.6.1.15,3.6.4.13
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

GIIETPRGAIKVTAQPTDHVVGEYLVLSPQTVLRSQKLSLIHALAEQVKTCTHSGRAGRYAVEAYDGRVLVPSGYAISPEDFQSLSESATMVYNEREFVNRKLHHIAMHGPALNTDEESYELVRAERTEHEYVYDVDQRRCCKKEEAAGLVLVGDLTNPPYHEFAYEGLKIRPACPYKIAVIGVFGVPGSGKSAIIKNLVTRQDLVTSGKKENCQEITTDVMRQRGLEISARTVDSLLLNGCNRPVDVLYVDEAFACHSGTLLALIALVRPRQKVVLCGDPKQCGFFNMMQMKVNYNHNICTQVYHKSISRRCTLPVTAIVSSLHYEGKMRTTNEYNKPIVVDTTGSTKPDPGDLVLTCFRGWVKQLQIDYRGHEVMTAAASQGLTRKGVYAVRQKVNENPLYASTSEHVNVLLTRTEGKLVWKTLSGDPWIKTLQNPPKGNFKATIKEWEVEHASIMAGICSHQMTFDTFQNKANVCWAKSLVPILETAGIKLNDRQWSQIIQAFKEDKAYSPEVALNEICTRMYGVDLDSGLFSKPLVSVYYADNHWDNRPGGKMFGFNPEAASILERKYPFTKGKWNINKQICVTTRRIEDFNPTTNIIPANRRLPHSLVAEHRPVKGERMEWLVNKINGHHVLLVSGCSLALPTKRVTWVAPLGVRGADYTYNLELGLPATLGRYDLVVINIHTPFRIHHYQQCVDHAMKLQMLGGDSLRLLKPGGSLLIRAYGYADRTSERVICVLGRKFRSSRALKPPCVTSNTEMFFLFSNFDNGRRNFTTHVMNNQLNAAFVGQATRAGC

Source Source

Source organism organism	Chikungunya virus strain S27-African prototype
NCBI taxonomy ID ncbi_taxonomy_id	371094
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	;RNA (5'-R(PCPCP*A)-3') ;
Molecular weight formula_weight	894.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	Z

CCA

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 7 Entity 7 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	12

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7y38Y01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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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	triclinic

Resolution resolution	2.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	132510

Molecular architecture of the chikungunya virus replication complex

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

mRNA-capping enzyme nsP1,affinity-tag (strepII-3XFLAG)

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

7y38__assembly_1__model_1

7y38__assembly_1__model_1 | I(q)

7y38__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 (7)

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

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Molecular architecture of the chikungunya virus replication complex

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

mRNA-capping enzyme nsP1,affinity-tag (strepII-3XFLAG)

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

7y38__assembly_1__model_1

7y38__assembly_1__model_1 | I(q)

7y38__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 (7)

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

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)