9n96

CRYO-EM STRUCTURE OF human U7 SM RING IN COMPLEX WITH SYMPLEKIN N-TERMINAL DOMAIN

Method: ELECTRON MICROSCOPY

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

Small nuclear ribonucleoprotein Sm D3

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 2	;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 （P14678） U7 snRNA-associated Sm-like protein LSm10 × 1 （Q969L4） U7 snRNA-associated Sm-like protein LSm11 × 1 Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308） Symplekin × 1 （Q92797） modified H2a pre-mRNA × 1 U7 snRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMD3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–146； UniProt 1–126

;Small nuclear ribonucleoprotein-associated proteins B and B' ;

Homo sapiens

UniProt P14678

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 2	Small nuclear ribonucleoprotein Sm D3 × 1 （P62318） U7 snRNA-associated Sm-like protein LSm10 × 1 （Q969L4） U7 snRNA-associated Sm-like protein LSm11 × 1 Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308） Symplekin × 1 （Q92797） modified H2a pre-mRNA × 1 U7 snRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RSMB_HUMAN
Isoform	P14678-2
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–95； UniProt 1–95

U7 snRNA-associated Sm-like protein LSm10

Homo sapiens

UniProt Q969L4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 2	Small nuclear ribonucleoprotein Sm D3 × 1 （P62318） ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 （P14678） U7 snRNA-associated Sm-like protein LSm11 × 1 Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308） Symplekin × 1 （Q92797） modified H2a pre-mRNA × 1 U7 snRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LSM10_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–123； UniProt 1–123

Small nuclear ribonucleoprotein E

Homo sapiens

UniProt P62304

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 2	Small nuclear ribonucleoprotein Sm D3 × 1 （P62318） ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 （P14678） U7 snRNA-associated Sm-like protein LSm10 × 1 （Q969L4） U7 snRNA-associated Sm-like protein LSm11 × 1 Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308） Symplekin × 1 （Q92797） modified H2a pre-mRNA × 1 U7 snRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RUXE_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–92； UniProt 1–92

Small nuclear ribonucleoprotein F

Homo sapiens

UniProt P62306

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 2	Small nuclear ribonucleoprotein Sm D3 × 1 （P62318） ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 （P14678） U7 snRNA-associated Sm-like protein LSm10 × 1 （Q969L4） U7 snRNA-associated Sm-like protein LSm11 × 1 Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein G × 1 （P62308） Symplekin × 1 （Q92797） modified H2a pre-mRNA × 1 U7 snRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RUXF_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–86； UniProt 1–86

Small nuclear ribonucleoprotein G

Homo sapiens

UniProt P62308

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 2	Small nuclear ribonucleoprotein Sm D3 × 1 （P62318） ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 （P14678） U7 snRNA-associated Sm-like protein LSm10 × 1 （Q969L4） U7 snRNA-associated Sm-like protein LSm11 × 1 Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） Symplekin × 1 （Q92797） modified H2a pre-mRNA × 1 U7 snRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RUXG_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain G； PDBConstruct 1–76； UniProt 1–76

Symplekin

Homo sapiens

UniProt Q92797

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 2	Small nuclear ribonucleoprotein Sm D3 × 1 （P62318） ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 （P14678） U7 snRNA-associated Sm-like protein LSm10 × 1 （Q969L4） U7 snRNA-associated Sm-like protein LSm11 × 1 Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308） modified H2a pre-mRNA × 1 U7 snRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYMPK_HUMAN
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain J； PDBConstruct 1–1072； UniProt 30–1101

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	9n96
Deposition date deposition_date	2025-02-10
Structure title title	CRYO-EM STRUCTURE OF human U7 SM RING IN COMPLEX WITH SYMPLEKIN N-TERMINAL DOMAIN
Keywords keywords	;Symplekin, 3' end processing, U7 snRNP, Histone pre-mRNA, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA complex ;; RNA BINDING 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.

9n96__assembly_1__model_1

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

Download this curve (.dat)

9n96__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9n96__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.67 Å
Rg (electron density)	33.64 Å
Total Rg	34.04 Å
Atom count	7921
Residues	922
Excluded volume	139140 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9n96__assembly_1__model_1`	decameric （10）	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 (10)

Entity 1 Entity 1 polymer

Description description	Small nuclear ribonucleoprotein Sm D3
Molecular weight formula_weight	16111.7 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	7921

MGSSHHHHHHSSGLVPRGSHMSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGNIFQKRR

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;Small nuclear ribonucleoprotein-associated proteins B and B' ;
Molecular weight formula_weight	10911.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARV

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	U7 snRNA-associated Sm-like protein LSm10
Molecular weight formula_weight	14102.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MAVSHSVKERTISENSLIILLQGLQGRVTTVDLRDESVAHGRIDNVDAFMNIRLAKVTYTDRWGHQVKLDDLFVTGRNVRYVHIPDDVNITSTIEQQLQIIHRVRNFGGKGQGRWEFPPKNCK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 4 Entity 4 polymer

Description description	U7 snRNA-associated Sm-like protein LSm11
Molecular weight formula_weight	28399.3 kDa
Mutation mutation	R109E, I110A, R112E, L113A, R114E, L116A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MHHHHHHSGGSMEERERGARSAGAGSPARPPSPRLDVSSDSFDPLLALYAPRLPPIPYPNAPCFNNVAEYESFLRTGVRGGGRGRGRARGAAAGSGVPAAPGPSGRTRRRPDAPAPDPEEAQEAERAMVAKEEGDGAAGAGRRGPGRSRKAPRNVLTRMPLHEGSPLGELHRCIREGVKVNVHIRTFKGLRGVCTGFLVAFDKFWNMALTDVDETYRKPVLQSRKKKRKPKVDYQQVFTRHINQIFIRGENVLLVHLAQ

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 5 Entity 5 polymer

Description description	Small nuclear ribonucleoprotein E
Molecular weight formula_weight	10817.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQSVSN

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 polymer

Description description	Small nuclear ribonucleoprotein F
Molecular weight formula_weight	9734.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVEEEEEDGEMRE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 7 Entity 7 polymer

Description description	Small nuclear ribonucleoprotein G
Molecular weight formula_weight	9579.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIMLEALERVLEHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 8 Entity 8 polymer

Description description	Symplekin
Molecular weight formula_weight	120355.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MTTSERVVDLLNQAALITNDSKITVLKQVQELIINKDPTLLDNFLDEIIAFQADKSIEVRKFVIGFIEEACKRDIELLLKLIANLNMLLRDENVNVVKKAILTMTQLYKVALQWMVKSRVISELQEACWDMVSAMAGDIILLLDSDNDGIRTHAIKFVEGLIVTLSPRMADSEIPRRQEHDISLDRIPRDHPYIQYNVLWEEGKAALEQLLKFMVHPAISSINLTTALGSLANIARQRPMFMSEVIQAYETLHANLPPTLAKSQVSSVRKNLKLHLLSVLKHPASLEFQAQITTLLVDLGTPQAEIARNMPSSKDTRKRPRDDSDSTLKKMKLEPNLGEDDEDKDLEPGPSGTSKASAQISGQSDTDITAEFLQPLLTPDNVANLVLISMVYLPEAMPASFQAIYTPVESAGTEAQIKHLARLMATQMTAAGLGPGVEQTKQCKEEPKEEKVVKTESVLIKRRLSAQGQAISVVGSLSSMSPLEEEAPQAKRRPEPIIPVTQPRLAGAGGRKKIFRLSDVLKPLTDAQVEAMKLGAVKRILRAEKAVACSGAAQVRIKILASLVTQFNSGLKAEVLSFILEDVRARLDLAFAWLYQEYNAYLAAGASGSLDKYEDCLIRLLSGLQEKPDQKDGIFTKVVLEAPLITESALEVVRKYCEDESRTYLGMSTLRDLIFKRPSRQFQYLHVLLDLSSHEKDKVRSQALLFIKRMYEKEQLREYVEKFALNYLQLLVHPNPPSVLFGADKDTEVAAPWTEETVKQCLYLYLALLPQNHKLIHELAAVYTEAIADIKRTVLRVIEQPIRGMGMNSPELLLLVENCPKGAETLVTRCLHSLTDKVPPSPELVKRVRDLYHKRLPDVRFLIPVLNGLEKKEVIQALPKLIKLNPIVVKEVFNRLLGTQHGEGNSALSPLNPGELLIALHNIDSVKCDMKSIIKATNLCFAERNVYTSEVLAVVMQQLMEQSPLPMLLMRTVIQSLTMYPRLGGFVMNILSRLIMKQVWKYPKVWEGFIKCCQRTKPQSFQVILQLPPQQLGAVFDKCPELREPLLAHVRSFTPHQQAHIPNSIMTILEAS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 9 Entity 9 polymer

Description description	modified H2a pre-mRNA
Molecular weight formula_weight	19237.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	Y

CCAAAGGCUCUUUUCAGAGCCACCCACUGAAUCAGAUAAAGAGCUGUAACACGGUAGCCA

Entity 10 Entity 10 polymer

Description description	U7 snRNA
Molecular weight formula_weight	20013.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	Z

CAGUGUUACAGCUCUUUUAGAAUUUGUCUAGUAGGCUUUCUGGCUUUUUACCGGAAAGCCCCU

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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	3.180 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.18 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	236295

CRYO-EM STRUCTURE OF human U7 SM RING IN COMPLEX WITH SYMPLEKIN N-TERMINAL DOMAIN

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

Small nuclear ribonucleoprotein Sm D3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;Small nuclear ribonucleoprotein-associated proteins B and B' ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

U7 snRNA-associated Sm-like protein LSm10

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small nuclear ribonucleoprotein E

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small nuclear ribonucleoprotein F

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small nuclear ribonucleoprotein G

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Symplekin

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

9n96__assembly_1__model_1

9n96__assembly_1__model_1 | I(q)

9n96__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (10)

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