SAXSdb — 9qb3

▼

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

H/ACA ribonucleoprotein complex subunit DKC1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 18 RNA 2	H/ACA ribonucleoprotein complex subunit 1 × 4 （Q9NY12） H/ACA ribonucleoprotein complex subunit 2 × 4 （Q9NX24） H/ACA ribonucleoprotein complex subunit 3 × 4 （Q9NPE3） Telomerase Cajal body protein 1 × 2 （Q9BUR4） hTR, human telomerase RNA × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DKC1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–514； UniProt 1–514 Author chain G； PDBConstruct 1–514； UniProt 1–514 Author chain c； PDBConstruct 1–514； UniProt 1–514 Author chain g； PDBConstruct 1–514； UniProt 1–514

H/ACA ribonucleoprotein complex subunit 1

OrganismNot specified

UniProt Q9NY12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 18 RNA 2	H/ACA ribonucleoprotein complex subunit DKC1 × 4 （O60832） H/ACA ribonucleoprotein complex subunit 2 × 4 （Q9NX24） H/ACA ribonucleoprotein complex subunit 3 × 4 （Q9NPE3） Telomerase Cajal body protein 1 × 2 （Q9BUR4） hTR, human telomerase RNA × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GAR1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–217； UniProt 1–217 Author chain H； PDBConstruct 1–217； UniProt 1–217 Author chain d； PDBConstruct 1–217； UniProt 1–217 Author chain h； PDBConstruct 1–217； UniProt 1–217

H/ACA ribonucleoprotein complex subunit 2

OrganismNot specified

UniProt Q9NX24

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 18 RNA 2	H/ACA ribonucleoprotein complex subunit DKC1 × 4 （O60832） H/ACA ribonucleoprotein complex subunit 1 × 4 （Q9NY12） H/ACA ribonucleoprotein complex subunit 3 × 4 （Q9NPE3） Telomerase Cajal body protein 1 × 2 （Q9BUR4） hTR, human telomerase RNA × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NHP2_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–153； UniProt 1–153 Author chain I； PDBConstruct 1–153； UniProt 1–153 Author chain e； PDBConstruct 1–153； UniProt 1–153 Author chain i； PDBConstruct 1–153； UniProt 1–153

H/ACA ribonucleoprotein complex subunit 3

OrganismNot specified

UniProt Q9NPE3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 18 RNA 2	H/ACA ribonucleoprotein complex subunit DKC1 × 4 （O60832） H/ACA ribonucleoprotein complex subunit 1 × 4 （Q9NY12） H/ACA ribonucleoprotein complex subunit 2 × 4 （Q9NX24） Telomerase Cajal body protein 1 × 2 （Q9BUR4） hTR, human telomerase RNA × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NOP10_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–64； UniProt 1–64 Author chain J； PDBConstruct 1–64； UniProt 1–64 Author chain f； PDBConstruct 1–64； UniProt 1–64 Author chain j； PDBConstruct 1–64； UniProt 1–64

Telomerase Cajal body protein 1

OrganismNot specified

UniProt Q9BUR4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 18 RNA 2	H/ACA ribonucleoprotein complex subunit DKC1 × 4 （O60832） H/ACA ribonucleoprotein complex subunit 1 × 4 （Q9NY12） H/ACA ribonucleoprotein complex subunit 2 × 4 （Q9NX24） H/ACA ribonucleoprotein complex subunit 3 × 4 （Q9NPE3） hTR, human telomerase RNA × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TCAB1_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain K； PDBConstruct 1–548； UniProt 1–548 Author chain k； PDBConstruct 1–548； UniProt 1–548

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9qb3
Deposition date deposition_date	2025-02-28
Structure title title	Dimer structure of H/ACA RNP lobe of human telomerase
Keywords keywords	telomerase, H/ACA, RNA-binding protein, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

9qb3__assembly_1__model_1

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

Download this curve (.dat)

9qb3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9qb3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	59.80 Å
Rg (electron density)	59.05 Å
Total Rg	59.20 Å
Atom count	34722
Residues	3720
Excluded volume	592260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9qb3__assembly_1__model_1`	20-meric （20）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	H/ACA ribonucleoprotein complex subunit DKC1
Molecular weight formula_weight	57779.2 kDa
EC 编号 ec_number	5.4.99.-
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G,c,g
Atom count atom_count	34722

MADAEVIILPKKHKKKKERKSLPEEDVAEIQHAEEFLIKPESKVAKLDTSQWPLLLKNFDKLNVRTTHYTPLACGSNPLKREIGDYIRTGFINLDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRLHNAIEGGTQLSRALETLTGALFQRPPLIAAVKRQLRVRTIYESKMIEYDPERRLGIFWVSCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVMSEKDHMVTMHDVLDAQWLYDNHKDESYLRRVVYPLEKLLTSHKRLVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQEIVVITTKGEAICMAIALMTTAVISTCDHGIVAKIKRVIMERDTYPRKWGLGPKASQKKLMIKQGLLDKHGKPTDSTPATWKQEYVDYSESAKKEVVAEVVKAPQVVAEAAKTAKRKRESESESDETPPAAPQLIKKEKKKSKKDKKAKAGLESGAEPGDGDSDTTKKKKKKKKAKEVELVSE

Entity 2 Entity 2 polymer

Description description	H/ACA ribonucleoprotein complex subunit 1
Molecular weight formula_weight	22388.0 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H,d,h

MSFRGGGRGGFNRGGGGGGFNRGGSSNHFRGGGGGGGGGNFRGGGRGGFGRGGGRGGFNKGQDQGPPERVVLLGEFLHPCEDDIVCKCTTDENKVPYFNAPVYLENKEQIGKVDEIFGQLRDFYFSVKLSENMKASSFKKLQKFYIDPYKLLPLQRFLPRPPGEKGPPRGGGRGGRGGGRGGGGRGGGRGGGFRGGRGGGGGGFRGGRGGGFRGRGH

Entity 3 Entity 3 polymer

Description description	H/ACA ribonucleoprotein complex subunit 2
Molecular weight formula_weight	17226.1 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,I,e,i

MTKIKADPDGPEAQAEACSGERTYQELLVNQNPIAQPLASRRLTRKLYKCIKKAVKQKQIRRGVKEVQKFVNKGEKGIMVLAGDTLPIEVYCHLPVMCEDRNLPYVYIPSKTDLGAAAGSKRPTCVIMVKPHEEYQEAYDECLEEVQSLPLPL

Entity 4 Entity 4 polymer

Description description	H/ACA ribonucleoprotein complex subunit 3
Molecular weight formula_weight	7720.0 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,J,f,j

MFLQYYLNEQGDRVYTLKKFDPMGQQTCSAHPARFSPDDKYSRHRITIKKRFKVLMTQQPRPVL

Entity 5 Entity 5 polymer

Description description	Telomerase Cajal body protein 1
Molecular weight formula_weight	59357.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K,k

MKTLETQPLAPDCCPSDQDPAPAHPSPHASPMNKNADSELMPPPPERGDPPRLSPDPVAGSAVSQELREGDPVSLSTPLETEFGSPSELSPRIEEQELSENTSLPAEEANGSLSEEEANGPELGSGKAMEDTSGEPAAEDEGDTAWNYSFSQLPRFLSGSWSEFSTQPENFLKGCKWAPDGSCILTNSADNILRIYNLPPELYHEGEQVEYAEMVPVLRMVEGDTIYDYCWYSLMSSAQPDTSYVASSSRENPIHIWDAFTGELRASFRAYNHLDELTAAHSLCFSPDGSQLFCGFNRTVRVFSTARPGRDCEVRATFAKKQGQSGIISCIAFSPAQPLYACGSYGRSLGLYAWDDGSPLALLGGHQGGITHLCFHPDGNRFFSGARKDAELLCWDLRQSGYPLWSLGREVTTNQRIYFDLDPTGQFLVSGSTSGAVSVWDTDGPGNDGKPEPVLSFLPQKDCTNGVSLHPSLPLLATASGQRVFPEPTESGDEGEELGLPLLSTRHVHLECRLQLWWCGGAPDSSIPDDHQGEKGQGGTEGGVGELI

Entity 6 Entity 6 polymer

Description description	hTR, human telomerase RNA
Molecular weight formula_weight	145477.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B,b

GGGUUGCGGAGGGUGGGCCUGGGAGGGGUGGUGGCCAUUUUUUGUCUAACCCUAACUGAGAAGGGCGUAGGCGCCGUGCUUUUGCUCCCCGCGCGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGAAAAGCCUCGGCCUGCCGCCUUCCACCGUUCAUUCUAGAGCAAACAAAAAAUGUCAGCUGCUGGCCCGUUCGCCCCUCCCGGGGACCUGCGGCGGGUCGCCUGCCCAGCCCCCGAACCCCGCCUGGAGGCCGCGGUCGGCCCGGGGCUUCUCCGGAGGCACCCACUGCCACCGCGAAGAGUUGGGCUCUGUCAGCCGCGGGUCUCUCGGGGGCGAGGGCGAGGUUCAGGCCUUUCAGGCCGCAGGAAGAGGAACGGAGCGAGUCCCCGCGCGCGGCGCGAUUCCCUGAGCUGUGGGACGUGCACCCAGGACUCGGCUCACACAUGC

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

▶

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	3.900 Å
Low-resolution limit resolution_low	173.680 Å
R factor r_factor	0.3260
R_work r_work	0.3260
R_free r_free	—

Resolution resolution	3.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	88419

Dimer structure of H/ACA RNP lobe of human telomerase

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

H/ACA ribonucleoprotein complex subunit DKC1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

H/ACA ribonucleoprotein complex subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

H/ACA ribonucleoprotein complex subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

H/ACA ribonucleoprotein complex subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Telomerase Cajal body protein 1

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

9qb3__assembly_1__model_1

9qb3__assembly_1__model_1 | I(q)

9qb3__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 (6)

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

Source Source

7. Citations (1)