9gcl

Structure of the U11 snRNP C-lobe

Method: ELECTRON MICROSCOPY

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

Zinc finger matrin-type protein 5

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 1	Small nuclear ribonucleoprotein Sm D1 × 1 （P62314） Small nuclear ribonucleoprotein Sm D3 × 1 （P62318） ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 （P14678） Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308） U11/U12 small nuclear ribonucleoprotein 48 kDa protein × 1 （Q6IEG0） Small nuclear ribonucleoprotein Sm D2 × 1 （P62316） U11 snRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ZMAT5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 1–170； UniProt 1–170

Small nuclear ribonucleoprotein Sm D1

Homo sapiens

UniProt P62314

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 1	Zinc finger matrin-type protein 5 × 1 （Q9UDW3） Small nuclear ribonucleoprotein Sm D3 × 1 （P62318） ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 （P14678） Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308） U11/U12 small nuclear ribonucleoprotein 48 kDa protein × 1 （Q6IEG0） Small nuclear ribonucleoprotein Sm D2 × 1 （P62316） U11 snRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMD1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain h； PDBConstruct 1–119； UniProt 1–119

Small nuclear ribonucleoprotein Sm D3

Homo sapiens

UniProt P62318

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 1	Zinc finger matrin-type protein 5 × 1 （Q9UDW3） Small nuclear ribonucleoprotein Sm D1 × 1 （P62314） ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 （P14678） Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308） U11/U12 small nuclear ribonucleoprotein 48 kDa protein × 1 （Q6IEG0） Small nuclear ribonucleoprotein Sm D2 × 1 （P62316） U11 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	3
Chains and sequence ranges	Author chain j； PDBConstruct 1–126； 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 9 RNA 1	Zinc finger matrin-type protein 5 × 1 （Q9UDW3） Small nuclear ribonucleoprotein Sm D1 × 1 （P62314） Small nuclear ribonucleoprotein Sm D3 × 1 （P62318） Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308） U11/U12 small nuclear ribonucleoprotein 48 kDa protein × 1 （Q6IEG0） Small nuclear ribonucleoprotein Sm D2 × 1 （P62316） U11 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	—
PDB entities	4
Chains and sequence ranges	Author chain k； PDBConstruct 1–240； UniProt 1–240

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 9 RNA 1	Zinc finger matrin-type protein 5 × 1 （Q9UDW3） Small nuclear ribonucleoprotein Sm D1 × 1 （P62314） Small nuclear ribonucleoprotein Sm D3 × 1 （P62318） ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 （P14678） Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308） U11/U12 small nuclear ribonucleoprotein 48 kDa protein × 1 （Q6IEG0） Small nuclear ribonucleoprotein Sm D2 × 1 （P62316） U11 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 l； 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 9 RNA 1	Zinc finger matrin-type protein 5 × 1 （Q9UDW3） Small nuclear ribonucleoprotein Sm D1 × 1 （P62314） Small nuclear ribonucleoprotein Sm D3 × 1 （P62318） ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 （P14678） Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein G × 1 （P62308） U11/U12 small nuclear ribonucleoprotein 48 kDa protein × 1 （Q6IEG0） Small nuclear ribonucleoprotein Sm D2 × 1 （P62316） U11 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 m； 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 9 RNA 1	Zinc finger matrin-type protein 5 × 1 （Q9UDW3） Small nuclear ribonucleoprotein Sm D1 × 1 （P62314） Small nuclear ribonucleoprotein Sm D3 × 1 （P62318） ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 （P14678） Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） U11/U12 small nuclear ribonucleoprotein 48 kDa protein × 1 （Q6IEG0） Small nuclear ribonucleoprotein Sm D2 × 1 （P62316） U11 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 n； PDBConstruct 1–76； UniProt 1–76

U11/U12 small nuclear ribonucleoprotein 48 kDa protein

Homo sapiens

UniProt Q6IEG0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 1	Zinc finger matrin-type protein 5 × 1 （Q9UDW3） Small nuclear ribonucleoprotein Sm D1 × 1 （P62314） Small nuclear ribonucleoprotein Sm D3 × 1 （P62318） ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 （P14678） Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308） Small nuclear ribonucleoprotein Sm D2 × 1 （P62316） U11 snRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SNR48_HUMAN
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain F； PDBConstruct 1–339； UniProt 1–339

Small nuclear ribonucleoprotein Sm D2

Homo sapiens

UniProt P62316

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 1	Zinc finger matrin-type protein 5 × 1 （Q9UDW3） Small nuclear ribonucleoprotein Sm D1 × 1 （P62314） Small nuclear ribonucleoprotein Sm D3 × 1 （P62318） ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 （P14678） Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308） U11/U12 small nuclear ribonucleoprotein 48 kDa protein × 1 （Q6IEG0） U11 snRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMD2_HUMAN
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain i； PDBConstruct 1–118； UniProt 1–118

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	9gcl
Deposition date deposition_date	2024-08-02
Structure title title	Structure of the U11 snRNP C-lobe
Keywords keywords	minor spliceosome, U11 snRNP, RNA-protein complex, SPLICING; SPLICING
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.

9gcl__assembly_1__model_1

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

Download this curve (.dat)

9gcl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9gcl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.09 Å
Rg (electron density)	29.92 Å
Total Rg	30.51 Å
Atom count	7307
Residues	830
Excluded volume	127010 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9gcl__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	Zinc finger matrin-type protein 5
Molecular weight formula_weight	20002.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E
Atom count atom_count	7307

MGKRYFCDYCDRSFQDNLHNRKKHLNGLQHLKAKKVWYDMFRDAAAILLDEQNKRPCRKFLLTGQCDFGSNCRFSHMSERDLQELSIQVEEERRAREWLLDAPELPEGHLEDWLEKRAKRLSSAPSSRAEPIRTTVFQYPVGWPPVQELPPSLRAPPPGGWPLQPRVQWG

Source Source

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

Entity 2 Entity 2 polymer

Description description	Small nuclear ribonucleoprotein Sm D1
Molecular weight formula_weight	13310.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	h

MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR

Source Source

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

Entity 3 Entity 3 polymer

Description description	Small nuclear ribonucleoprotein Sm D3
Molecular weight formula_weight	13940.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	j

MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGNIFQKRR

Source Source

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

Entity 4 Entity 4 polymer

Description description	;Small nuclear ribonucleoprotein-associated proteins B and B' ;
Molecular weight formula_weight	24642.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	k

MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGMRGPPPPGMRPPRP

Source Source

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

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	l

MAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQSVSN

Source Source

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

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	m

MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVEEEEEDGEMRE

Source Source

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

Entity 7 Entity 7 polymer

Description description	Small nuclear ribonucleoprotein G
Molecular weight formula_weight	8508.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	n

MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIMLEALERV

Source Source

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

Entity 8 Entity 8 polymer

Description description	U11/U12 small nuclear ribonucleoprotein 48 kDa protein
Molecular weight formula_weight	40042.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MEGEPPPVEERRRLQEELNEFVESGCRTLEEVTASLGWDLDSLDPGEEEAAEDEVVICPYDSNHHMPKSSLAKHMASCRLRKMGYTKEEEDEMYNPEFFYENVKIPSITLNKDSQFQIIKQARTAVGKDSDCYNQRIYSSLPVEVPLNHKRFVCDLTQADRLALYDFVVEETKKKRSDSQIIENDSDLFVDLAAKINQDNSRKSPKSYLEILAEVRDYKRRRQSYRAKNVHITKKSYTEVIRDVINVHMEELSNHWQEEQEKAEDDAEKNEERRSASVDSRQSGGSYLDAECSRHRRDRSRSPHKRKRNKDKDKNCESRRRKERDGERHHSHKRRKQKI

Source Source

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

Entity 9 Entity 9 polymer

Description description	Small nuclear ribonucleoprotein Sm D2
Molecular weight formula_weight	13551.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	i

MSLLNKPKSEMTPEELQKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNPLIAGK

Source Source

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

Entity 10 Entity 10 polymer

Description description	U11 snRNA
Molecular weight formula_weight	43497.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	A

AAAAAGGGCUUCUGUCGUGAGUGGCACACGUAGGGCAACUCGAUUGCUCUGCGUGCGGAAUCGACAUCAAGGGCUUUCGGAAGCAUAAUUUUUUGGUAUUUGGGCAGCUGGUGAUCGUUGGUCCCGGCGCCCUUU

Source Source

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

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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	3.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	222666

Structure of the U11 snRNP C-lobe

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

Zinc finger matrin-type protein 5

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 Sm D1

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 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

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

U11/U12 small nuclear ribonucleoprotein 48 kDa 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

Small nuclear ribonucleoprotein Sm D2

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

9gcl__assembly_1__model_1

9gcl__assembly_1__model_1 | I(q)

9gcl__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment