7m50

Crystallographic structure of a cubic crystal form of STMV grown from ammonium sulfate

Method: X-RAY DIFFRACTION

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

Coat protein

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 60 RNA 57	;RNA (5'-R(PAPAPAPAPAPAPAPA)-3') ; × 9 ;RNA (5'-R(PAPAPAPAPAPA)-3') ; × 6 ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 9 ;RNA (5'-R(PUPUPUPUPUPUPU)-3') ; × 6 ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPUPUPU))-3') ; × 6 ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 3 ;RNA (5'-R(PUPUPUPUPUPUPUPUPU)-3') ; × 9 ;RNA (5'-R(PUPUPUPUPUPUPUPU)-3') ; × 9 PHOSPHATE ION × 15 MAGNESIUM ION × 15 CHLORIDE ION × 3 SULFATE ION × 18 water × 117	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COAT_STMV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–159； UniProt 1–159 Author chain B； PDBConstruct 1–159； UniProt 1–159 Author chain C； PDBConstruct 1–159； UniProt 1–159 Author chain D； PDBConstruct 1–159； UniProt 1–159 Author chain E； PDBConstruct 1–159； UniProt 1–159 Author chain F； PDBConstruct 1–159； UniProt 1–159 Author chain G； PDBConstruct 1–159； UniProt 1–159 Author chain GG； PDBConstruct 1–159； UniProt 1–159 Author chain H； PDBConstruct 1–159； UniProt 1–159 Author chain HH； PDBConstruct 1–159； UniProt 1–159 Author chain I； PDBConstruct 1–159； UniProt 1–159 Author chain II； PDBConstruct 1–159； UniProt 1–159 Author chain J； PDBConstruct 1–159； UniProt 1–159 Author chain JJ； PDBConstruct 1–159； UniProt 1–159 Author chain K； PDBConstruct 1–159； UniProt 1–159 Author chain KK； PDBConstruct 1–159； UniProt 1–159 Author chain L； PDBConstruct 1–159； UniProt 1–159 Author chain M； PDBConstruct 1–159； UniProt 1–159 Author chain N； PDBConstruct 1–159； UniProt 1–159 Author chain O； PDBConstruct 1–159； UniProt 1–159

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	7m50
Deposition date deposition_date	2021-03-22
Structure title title	Crystallographic structure of a cubic crystal form of STMV grown from ammonium sulfate
Keywords keywords	RNA, ions, ion channel, decapsidation, VIRUS; VIRUS
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.

7m50__assembly_1__model_1

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

Download this curve (.dat)

7m50__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7m50__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	70.80 Å
Rg (electron density)	71.26 Å
Total Rg	71.23 Å
Atom count	76385
Residues	9147
Excluded volume	1324600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7m50__assembly_1__model_1`	117-meric （117）	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 (14)

Entity 1 Entity 1 polymer

Description description	Coat protein
Molecular weight formula_weight	17533.9 kDa
Source method src_method	nat
Copy count entity_count	20

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,GG,HH,II,JJ,KK
Atom count atom_count	29786

MGRGKVKPNRKSTGDNSNVVTMIRAGSYPKVNPTPTWVRAIPFEVSVQSGIAFKVPVGSLFSANFRTDSFTSVTVMSVRAWTQLTPPVNEYSFVRLKPLFKTGDSTEEFEGRASNINTRASVGYRIPTNLRQNTVAADNVCEVRSNCRQVALVISCCFN

Entity 2 Entity 2 polymer

Description description	;RNA (5'-R(PAPAPAPAPAPAPAPA)-3') ;
Molecular weight formula_weight	2588.7 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	P,V,TT

AAAAAAAA

Entity 3 Entity 3 polymer

Description description	;RNA (5'-R(PAPAPAPAPAPA)-3') ;
Molecular weight formula_weight	1930.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	S,T

AAAAAA

Entity 4 Entity 4 polymer

Description description	;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ;
Molecular weight formula_weight	3247.1 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	X,UU,bb

AAAAAAAAAA

Entity 5 Entity 5 polymer

Description description	;RNA (5'-R(PUPUPUPUPUPUP*U)-3') ;
Molecular weight formula_weight	2259.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	Y,a

AAAAAAA

Entity 6 Entity 6 polymer

Description description	;RNA (5'-R(PUPUPUPUPUPUPUPUPUPUPUPU))-3') ;
Molecular weight formula_weight	3629.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	e,WW

UUUUUUUUUUUU

Entity 7 Entity 7 polymer

Description description	;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ;
Molecular weight formula_weight	3016.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	h

UUUUUUUUUU

Entity 8 Entity 8 polymer

Description description	;RNA (5'-R(PUPUPUPUPUPUPUPUP*U)-3') ;
Molecular weight formula_weight	2710.5 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	i,ll,qq

UUUUUUUUU

Entity 9 Entity 9 polymer

Description description	;RNA (5'-R(PUPUPUPUPUPUPUPU)-3') ;
Molecular weight formula_weight	2404.4 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	m,n,kk

UUUUUUUU

Entity 10 Entity 10 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 11 Entity 11 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	nat
Copy count entity_count	5

Entity 12 Entity 12 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 13 Entity 13 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 14 Entity 14 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4318

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Unit-cell length a length_a	234.050 Å
Unit-cell length b length_b	234.050 Å
Unit-cell length c length_c	234.050 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	240

Space group space_group	P 2 3
Space-group number int_tables_number	195
Crystal system crystal_system	cubic

Resolution resolution	2.310 Å
Low-resolution limit resolution_low	74.010 Å
R factor r_factor	0.2484
R_work r_work	0.2459
R_free r_free	0.2708

Crystallographic structure of a cubic crystal form of STMV grown from ammonium sulfate

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

Coat protein

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

7m50__assembly_1__model_1

7m50__assembly_1__model_1 | I(q)

7m50__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 (14)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 polymer

Polymer Polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 non-polymer

Entity 14 Entity 14 water

7. Citations (1)

Crystallographic structure of a cubic crystal form of STMV grown from ammonium sulfate

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

Coat protein

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

7m50__assembly_1__model_1

7m50__assembly_1__model_1 | I(q)

7m50__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 (14)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 polymer

Polymer Polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 non-polymer

Entity 14 Entity 14 water

7. Citations (1)