SAXSdb — 9zs4

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

CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)

Serratia

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 10 RNA 2 PDB declaration: 12-meric（12） Consistent with all polymer counts	Chain A； UniProt 1–816	Not recorded	crRNA × 1 Target RNA × 1 CRISPR system Cms protein Csm2 × 3 （A0A2I5TBC8） CRISPR system Cms endoribonuclease Csm3 × 4 （A0A2I5TNQ0） CRISPR system Cms protein Csm4 × 1 （A0A2I5TQV2） CRISPR system Cms protein Csm5 × 1 （A0A2I5TBB3）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9ZS4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9ZS2 S. marcescens Cas10-Csm unbound to target RNA Deposited 2025-12-22	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric	Chain A 1–816（816 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A2I5TNR6_SERS3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–816； UniProt 1–816

CRISPR system Cms protein Csm2

Serratia

UniProt A0A2I5TBC8

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 10 RNA 2 PDB declaration: 12-meric（12） Consistent with all polymer counts	Chain B； UniProt 2–127 Chain C； UniProt 2–127 Chain D； UniProt 2–127	Not recorded	CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) × 1 （A0A2I5TNR6） crRNA × 1 Target RNA × 1 CRISPR system Cms endoribonuclease Csm3 × 4 （A0A2I5TNQ0） CRISPR system Cms protein Csm4 × 1 （A0A2I5TQV2） CRISPR system Cms protein Csm5 × 1 （A0A2I5TBB3）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A2I5TBC8_SERS3
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 8–133； UniProt 2–127 Author chain C； PDBConstruct 8–133； UniProt 2–127 Author chain D； PDBConstruct 8–133； UniProt 2–127

CRISPR system Cms endoribonuclease Csm3

Serratia

UniProt A0A2I5TNQ0

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 10 RNA 2 PDB declaration: 12-meric（12） Consistent with all polymer counts	Chain E； UniProt 1–248 Chain F； UniProt 1–248 Chain G； UniProt 1–248 Chain H； UniProt 1–248	Mutation：D34A	CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) × 1 （A0A2I5TNR6） crRNA × 1 Target RNA × 1 CRISPR system Cms protein Csm2 × 3 （A0A2I5TBC8） CRISPR system Cms protein Csm4 × 1 （A0A2I5TQV2） CRISPR system Cms protein Csm5 × 1 （A0A2I5TBB3）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9ZS4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9ZS2 S. marcescens Cas10-Csm unbound to target RNA Deposited 2025-12-22	Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric	Chain E 1–248（248 aa） Chain F 1–248（248 aa） Chain G 1–248（248 aa） Chain H 1–248（248 aa）	Mutation：D43A Mutation：D43A Mutation：D43A Mutation：D43A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A2I5TNQ0_SERS3
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–248； UniProt 1–248 Author chain F； PDBConstruct 1–248； UniProt 1–248 Author chain G； PDBConstruct 1–248； UniProt 1–248 Author chain H； PDBConstruct 1–248； UniProt 1–248

CRISPR system Cms protein Csm4

Serratia

UniProt A0A2I5TQV2

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 10 RNA 2 PDB declaration: 12-meric（12） Consistent with all polymer counts	Chain I； UniProt 1–326	Not recorded	CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) × 1 （A0A2I5TNR6） crRNA × 1 Target RNA × 1 CRISPR system Cms protein Csm2 × 3 （A0A2I5TBC8） CRISPR system Cms endoribonuclease Csm3 × 4 （A0A2I5TNQ0） CRISPR system Cms protein Csm5 × 1 （A0A2I5TBB3）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9ZS4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9ZS2 S. marcescens Cas10-Csm unbound to target RNA Deposited 2025-12-22	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric	Chain I 1–326（326 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A2I5TQV2_SERS3
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain I； PDBConstruct 1–326； UniProt 1–326

CRISPR system Cms protein Csm5

Serratia

UniProt A0A2I5TBB3

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 10 RNA 2 PDB declaration: 12-meric（12） Consistent with all polymer counts	Chain J； UniProt 1–559	Not recorded	CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) × 1 （A0A2I5TNR6） crRNA × 1 Target RNA × 1 CRISPR system Cms protein Csm2 × 3 （A0A2I5TBC8） CRISPR system Cms endoribonuclease Csm3 × 4 （A0A2I5TNQ0） CRISPR system Cms protein Csm4 × 1 （A0A2I5TQV2）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9ZS4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9ZS2 S. marcescens Cas10-Csm unbound to target RNA Deposited 2025-12-22	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric	Chain J 1–559（559 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A2I5TBB3_SERS3
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain J； PDBConstruct 1–559； UniProt 1–559

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	9zs4
Deposition date deposition_date	2025-12-22
Structure title title	S. marcescens Cas10-Csm bound to target RNA
Keywords keywords	CRISPR, crRNA, Cas10, type III, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	56.03 Å
Radius of gyration Rg (electron density) rg_electron	57.10 Å
Forward intensity I(0) i0	1828300000.00
Molecular weight molecular_weight	340340.0 kDa
Excluded volume excluded_volume	419080 Å³
Envelope volume envelope_volume	614790 Å³
Hydration-shell volume shell_volume	92902 Å³
Envelope diameter envelope_diameter	205.9 Å
Shell Rg shell_rg	54.95 Å
Envelope Rg envelope_rg	57.46 Å
Shape Rg shape_rg	57.11 Å
Total Rg total_rg	57.02 Å
Total atoms total_atoms	23910
Residues n_residues	2930
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	194.1 Å
Rg (real space) rg_real	56.57 Å
Rg uncertainty (real space) rg_real_error	2.19 Å
I(0) (real space) i0_real	1.8280e+09
I(0) uncertainty (real space) i0_real_error	3.6390e+07
Rg (reciprocal space) rg_reciprocal	55.57 Å
I(0) (reciprocal space) i0_reciprocal	1826000000.0000
Solution quality estimate total_estimate	0.7883
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	48.5 Å
Skewness Skewness skewness	0.588
Kurtosis Kurtosis kurtosis	-0.287
Angular range angular_range	— – 0.1400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	545900000.0000
Real-space data points n_real_points	29
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.677; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.861; Smooth: 0.353

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
Molecular weight formula_weight	90390.7 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	23910

MNWLAASCHVAAFALLHNLKPLAQRAGIQDFPSPALANKLFAPLPESLSARADLHENTLTLLLDFAARLARGLPETPVSRGETGLIPLTHLLADDNHSAPAERCYSPLAPLGVDSLMPVTAALPTGERQAAYRQVYQALIEGLEAIPAAHRLQPSLWLDHLDSLWMTTCHALPDGDGASGISLYDQGKTTAALAVALWQHHARQATPEKEISLTPGDDARLLLIQADVFGIQELIFAQGNQTQKMAAKLLRGRSFQVSLLAETAALRVLETFDLPPVCQLINAAGKSLIVAPNLPDAAERLAGLRQRLDEWFLTHTYAQTGIGLCSTVAGSAEFLGEQAYGRLQNRLAQAMEQQKYQRFSLCAGDAPPPVFEGYLDQIAQGAGGEPCPMNGLHPVETTLNGLGCSRLAADQITLGHWINHGHWISHGERYARLLILRDSTATFSDDRCLHLTLFGYQVVAVSLKEDSGEFGELACNGSLRRCWDVSLPPEGTSLFQGYARRFINGWMPLAQGEYQPECYPGIEEALANGDIKTFDHLSCEDLYQDADQSLRGTCALGVLKGDIDNLGHLFRSGLPQPGFAKTIGLSRQIHLFFTLWLPHLCRKDPRFANTYTVFAGGDDFFLIGPWRSQQTLALTMAQDFARYSGHNPALHFSLGLVQAKPGYPVRALAAQAEAALKQAKQHPGKNAICLYNEVMGWPEYDALLACSEELARWREHDGYPLSSGLLYRLLALSEQSAEESEKPQAALWRSRLAYFLRRNLVDNVKVPTKENPAAFRHQLHLELFEKLEQHLKRHRQRYRVALQRHLYHYRTVPRGE

来源 Source

来源生物 organism	Serratia
NCBI Class编号 ncbi_taxonomy_id	613
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	crRNA
Molecular weight formula_weight	13361.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	K

AUUAAGACCAUUUACAGAACCUGUUCCACUUAAUGAAGUUGC

Entity 3 Entity 3 polymer

Description description	Target RNA
Molecular weight formula_weight	13560.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	L

GCAACUUCAUUAAGUGGAACAGGUUCUGUAAAUGCGGAAGUA

Entity 4 Entity 4 polymer

Description description	CRISPR system Cms protein Csm2
Molecular weight formula_weight	15886.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MHHHHHHTTLDYFKRQLHKPEATFFDDDAQKFAEQLAQYGKKGKPTQLRRFYDQLQQLEQRINGDEEKLALYLPEIRMISAHLAYAKGRELISDEFCQTMQNLIRSINTCQHLKNGRLFFEATLGFLRAIRRD

来源 Source

来源生物 organism	Serratia
NCBI Class编号 ncbi_taxonomy_id	613
宿主生物 host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	CRISPR system Cms endoribonuclease Csm3
Molecular weight formula_weight	27185.9 kDa
Mutation mutation	D34A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MQLNNIQTLRATLVCETGLHIGGGDTALQIGGIASAVVRHPLTQQPYIPGSSLKGKLRSLLEWRAGVVGDTEGKVLSHQVYQQLIDDKKQAQALQALKILQLFGVSGGDKLSAEQAQQIGPTRLSFWDCEFDEHWLAQQGGRVQTEEKAENCIDRISGVALHPRFIERVPAGSRFDFRLTVRQLDGDSPDLLDTLLAGLKMLELDGLGGSISRGYGKVRFEALTLDGKDLQPRFEQLQPFKHTTQGAG

来源 Source

来源生物 organism	Serratia
NCBI Class编号 ncbi_taxonomy_id	613
宿主生物 host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	CRISPR system Cms protein Csm4
Molecular weight formula_weight	35770.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MPSPVAPAAAWQWLRLRLLPDSAFATALRGDTLFGQLCWYLRESLGEAGLNALLAGYHDQRPFAVISDPMLADHLPRPHLPEHRLGFAAADARARKQRKQQCWLPLAFAHQPLAEWGAHLTAAPEHHQHRSDVQMHNSINRQTLTTGGDDAFAPFGSEQHWFDVDTAWDLYLLHDKRLSAAQLTDALRAIGLLGYGKDASIGKGRFHLTPQPMPELPTPDGNPLRLTLAPCAPQQGHWHSADSFFSPLVRVGRHGAALVVQGHPFKNPLLLADSAAVLAPVTPDNRPFVGQGLGGNGRLSTALPQTVHQGYAPVIPVRFHHKAQPQ

来源 Source

来源生物 organism	Serratia
NCBI Class编号 ncbi_taxonomy_id	613
宿主生物 host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	CRISPR system Cms protein Csm5
Molecular weight formula_weight	63148.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MTRDQTPRRHTACDSDNMQYFTLTCLSPVHVATGDSLNPGEYLIDENALYELGQGGLSPALTATQRSELLTILESNDPALPLTVQRFLAREAGKLKYAARRMCPLLPGISRYYQSRLGQVMQNDTKNKKQMINQLELMRHVGAALGAPYIPGSTLKGAIRTALVSALNQGQPLQAERRETDKLSSKVAQDAERQLLGFDTRRDSPRYRIEHDPFHWLQVGDAVSPAEHPPMLDYWLVRRQPFKRTEKQDNKADNMELSPVECLKPRQSPLHCQITVKTPPTALAIKNPRLKQWLGKVSQLAQQVNRITLPQCHHELAWLAEKHIGTDDVYAPGQNWVAQMQQLLRQLDDPLQRGEALLLRVGKYGGAISKTVAGWRHIARLGRQGTRTTYHPDVTTCTLALPQADALTQALPFGWVLLHQPDQPEVTEFVASHHDWCQQQQQRLDAHQQQQHTHRQQRQQLAQAREEEAQRLADKARQSKARQSIMSLAEQLASEQTFQHKNPNGPLRGQLATCVGCVATEGSAEEKAELCTLFDDILNYWGIKPGKDKKLTALRNKLL

来源 Source

来源生物 organism	Serratia
NCBI Class编号 ncbi_taxonomy_id	613
宿主生物 host_organism	Escherichia coli

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8. Citations (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	triclinic

Resolution resolution	3.80 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	129762

fit	/app/data/saxs_computation/zs/9zs4/9zs4.fit
pddf	/app/data/pr_computation/zs/9zs4/9zs4.pr.out
profile	/app/data/saxs_computation/zs/9zs4/9zs4.dat

S. marcescens Cas10-Csm bound to target RNA

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

CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)

State in the Current Structure

Other States of the Same Protein in the Database

CRISPR system Cms protein Csm2

State in the Current Structure

Other States of the Same Protein in the Database

CRISPR system Cms endoribonuclease Csm3

State in the Current Structure

Other States of the Same Protein in the Database

CRISPR system Cms protein Csm4

State in the Current Structure

Other States of the Same Protein in the Database

CRISPR system Cms protein Csm5

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 polymer

Polymer Polymer

来源 Source

Entity 7 Entity 7 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)