SAXSdb — 5v5h

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

RNA-directed RNA polymerase L

Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin variant CC.2 × 1 SODIUM ION × 1 ZINC ION × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	L_CCHFI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–174； UniProt 1–169

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	5v5h
Deposition date deposition_date	2017-03-14
Structure title title	OTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ubiquitin variant CC.2
Keywords keywords	Ovarian Tumor Domain protease, deubiquitinase, ubiquitin variant, hydrolase, transferase; hydrolase, transferase
Experimental Method method	X-RAY DIFFRACTION

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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.

5v5h__assembly_1__model_1

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

Download this curve (.dat)

5v5h__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5v5h__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.50 Å
Rg (electron density)	18.37 Å
Total Rg	19.38 Å
Atom count	3784
Residues	241
Excluded volume	34327 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5v5h__assembly_1__model_1`	dimeric （2）	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 (6)

Entity 1 Entity 1 polymer

Description description	RNA-directed RNA polymerase L
Molecular weight formula_weight	19770.1 kDa
EC 编号 ec_number	3.4.19.12,2.7.7.48
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4041

GPLGSMDFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWTVAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFETDTREAL

Source Source

Source organism organism	Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970)
Common name common_name	CCHFV
NCBI taxonomy ID ncbi_taxonomy_id	652961
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Ubiquitin variant CC.2
Molecular weight formula_weight	12183.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MAHHHHHHVTSLYKKAGSTDYKDDDDKMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIRKQSNLYLLWRLGGWKK

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	223

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5v5hA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	80 —

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Unit-cell length a length_a	101.398 Å
Unit-cell length b length_b	33.599 Å
Unit-cell length c length_c	71.248 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.51 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	43.434 Å
R factor r_factor	0.1575
R_work r_work	0.1563
R_free r_free	0.1781

OTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ubiquitin variant CC.2

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

RNA-directed RNA polymerase L

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

5v5h__assembly_1__model_1

5v5h__assembly_1__model_1 | I(q)

5v5h__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

OTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ubiquitin variant CC.2

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

RNA-directed RNA polymerase L

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

5v5h__assembly_1__model_1

5v5h__assembly_1__model_1 | I(q)

5v5h__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)