SAXSdb — 3nvk

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

NOP5/NOP56 related protein

Pyrococcus furiosus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 4	50S ribosomal protein L7Ae × 2 （Q8U160） ;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ; × 2 （Q8U4M2） ;RNA (5'-R(GPCPCPGPUPUPGPAPAPGPCPUPCPUPGPAPCPCPGPAPAPAPGPGPCPGPUPGPAPUPGPAPGPC)-3') ; × 2 ;RNA (5'-R(GPAPGPCPUPUPCPAPAPCPGPGP*C)-3') ; × 2 S-ADENOSYLMETHIONINE × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8U4M1_PYRFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–373； UniProt 1–363 Author chain F； PDBConstruct 11–373； UniProt 1–363

50S ribosomal protein L7Ae

Pyrococcus furiosus

UniProt Q8U160

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 4	NOP5/NOP56 related protein × 2 （Q8U4M1） ;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ; × 2 （Q8U4M2） ;RNA (5'-R(GPCPCPGPUPUPGPAPAPGPCPUPCPUPGPAPCPCPGPAPAPAPGPGPCPGPUPGPAPUPGPAPGPC)-3') ; × 2 ;RNA (5'-R(GPAPGPCPUPUPCPAPAPCPGPGP*C)-3') ; × 2 S-ADENOSYLMETHIONINE × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL7A_PYRFU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 8–129； UniProt 2–123 Author chain H； PDBConstruct 8–129； UniProt 2–123

;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ;

Pyrococcus furiosus

UniProt Q8U4M2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 4	NOP5/NOP56 related protein × 2 （Q8U4M1） 50S ribosomal protein L7Ae × 2 （Q8U160） ;RNA (5'-R(GPCPCPGPUPUPGPAPAPGPCPUPCPUPGPAPCPCPGPAPAPAPGPGPCPGPUPGPAPUPGPAPGPC)-3') ; × 2 ;RNA (5'-R(GPAPGPCPUPUPCPAPAPCPGPGP*C)-3') ; × 2 S-ADENOSYLMETHIONINE × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FLPA_PYRFU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 8–234； UniProt 1–227 Author chain J； PDBConstruct 8–234； UniProt 1–227

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	3nvk
Deposition date deposition_date	2010-07-08
Structure title title	Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle
Keywords keywords	Nop domain kink turn methyl transferase, ribosome biogenesis spliceosome biogenesis, TRANSFERASE-RNA complex; TRANSFERASE/RNA
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.

3nvk__assembly_1__model_1

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

Download this curve (.dat)

3nvk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3nvk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.58 Å
Rg (electron density)	46.51 Å
Total Rg	46.59 Å
Atom count	12606
Residues	1476
Excluded volume	222170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3nvk__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 (6)

Entity 1 Entity 1 polymer

Description description	NOP5/NOP56 related protein
Molecular weight formula_weight	43470.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F
Atom count atom_count	12606

MHHHHHHVMIMKAFISENVRGIYAFDENGNLIEKRYFTDKPEKVLDQLLKGEITKDLEELLNSLKEKGYDEFVFEHPELSRRAKELGFSATTEFPNIAGERLRSNPEEFLGENWFEEYYKVGVALTRMRIQEQSGARDKMVIQAIEALDDVDKVINLLVARLREWYSLHFPELDELLPKHPQYVAFVKTVGHRDNINEEVLRELGLSEEKIKKILEAKEKTMGAWMDQTDIEVVRQLAEEIDRLYQLRKKLEDYIDRAMDDVAPNLKALVGAKLAARLISLAGGLRELAMMPSSTIQVLGAEKALFRHLRTGAKPPKHGVIYQYPAINRSPWWQRGKIARALAGKLAIAARVDYFSGEYIAEELKKELEARIRLVL

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	186497
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	50S ribosomal protein L7Ae
Molecular weight formula_weight	14243.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MHHHHHHAKPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVKELMK

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	186497
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ;
Molecular weight formula_weight	26760.8 kDa
EC 编号 ec_number	2.1.1.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J

MHHHHHHMVEVKKHKFPGVYVVIDDDGSEKIATKNLVPGQRVYGERVIKWEGEEYRIWNPHRSKLGAAIVNGLKNFPIKPGKSVLYLGIASGTTASHVSDIVGWEGKIYGIEFSPRVLRELVPIVEERRNIIPILGDATKPEEYRALVTKVDVIFEDVAQPTQAKILIDNAKAYLKRGGYGMIAVKSRSIDVTKEPEQVFKEVERELSEYFEVIERLNLEPYEKDHALFVVRKP

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	186497
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	;RNA (5'-R(GPCPCPGPUPUPGPAPAPGPCPUPCPUPGPAPCPCPGPAPAPAPGPGPCPGPUPGPAPUPGPAPGPC)-3') ;
Molecular weight formula_weight	11009.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	K,L

GCCGUUGAAGCUCUGACCGAAAGGCGUGAUGAGC

Entity 5 Entity 5 polymer

Description description	;RNA (5'-R(GPAPGPCPUPUPCPAPAPCPGPGP*C)-3') ;
Molecular weight formula_weight	4156.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	G,S

GAGCUUCAACGGC

Entity 6 Entity 6 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3nvkA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	220 —

Domain ID domain_id	3nvkA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	4070 —

Domain ID domain_id	3nvkA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	90 — Nop domain

Domain ID domain_id	3nvkE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	30 — Ribosomal protein L30/S12

Domain ID domain_id	3nvkF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	220 —

Domain ID domain_id	3nvkF02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	4070 —

Domain ID domain_id	3nvkF03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	90 — Nop domain

Domain ID domain_id	3nvkH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	30 — Ribosomal protein L30/S12

Domain ID domain_id	3nvkI01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3nvkI02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	3nvkJ01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3nvkJ02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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Unit-cell length a length_a	330.039 Å
Unit-cell length b length_b	94.548 Å
Unit-cell length c length_c	97.729 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.209 Å
Low-resolution limit resolution_low	39.690 Å
R factor r_factor	0.2361
R_work r_work	0.2304
R_free r_free	0.2878

Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle

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

NOP5/NOP56 related protein

State in the Current Structure

Other States of the Same Protein in the Database

50S ribosomal protein L7Ae

State in the Current Structure

Other States of the Same Protein in the Database

;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ;

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

3nvk__assembly_1__model_1

3nvk__assembly_1__model_1 | I(q)

3nvk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

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

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle

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

NOP5/NOP56 related 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

50S ribosomal protein L7Ae

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ;

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

3nvk__assembly_1__model_1

3nvk__assembly_1__model_1 | I(q)

3nvk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

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

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)