SAXSdb — 5nvr

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

Telomere length regulator protein RIF1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIF1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–1110； UniProt 177–1282

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	5nvr
Deposition date deposition_date	2017-05-04
Structure title title	Crystal structure of the Rif1 N-terminal domain (RIF1-NTD) from Saccharomyces cerevisiae
Keywords keywords	telomere maintenance, DNA double-strand break repair, irregular helical repeat, all-alpha fold, structural protein; STRUCTURAL PROTEIN
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.

5nvr__assembly_1__model_1

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

Download this curve (.dat)

5nvr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5nvr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	68.36 Å
Rg (electron density)	70.19 Å
Total Rg	69.72 Å
Atom count	17642
Residues	1050
Excluded volume	157980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5nvr__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5nvr__assembly_2__model_1`	dimeric （2）	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 (1)

Entity 1 Entity 1 polymer

Description description	Telomere length regulator protein RIF1
Molecular weight formula_weight	129054.0 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	17642

GGGRNIFTSPYKETRVNPRALEYWVSGEIHGLVDNESVSEFKEIIEGGLGILRQESEDYVARRFEVYATFNNIIPILTTKNVNEVDQKFNILIVNIESIIEICIPHLQIAQDTLLSSSEKKNPFVIRLYVQIVRFFSAIMSNFKIVKWLTKRPDLVNKLKVIYRWTTGALRNENSNKIIITAQVSFLRDEKFGTFFLSNEEIKPIISTFTEIMEINSHNLIYEKLLLIRGFLSKYPKLMIETVTSWLPGEVLPRIIIGDEIYSMKILITSIVVLLELLKKCLDFVDEHERIYQCIMLSPVCETIPEKFLSKLPLNSYDSANLDKVTIGHLLTQQIKNYIVVKNDNKIAMDLWLSMTGLLYDSGKRVYDLTSESNKVWFDLNNLCFINNHPKTRLMSIKVWRIITYCICTKISQKNQEGNKSLLSLLRTPFQMTLPYVNDPSAREGIIYHLLGVVYTAFTSNKNLSTDMFELFWDHLITPIYEDYVFKYDSIHLQNVLFTVLHLLIGGKNADVALERKYKKHIHPMSVIASEGVKLKDISSLPPQIIKREYDKIMKVVFQAVEVAISNVNLAHDLILTSLKHLPEDRKDQTHLESFSSLILKVTQNNKDTPIFRDFFGAVTSSFVYTFLDLFLRKNDSSLVNFNIQISKVGISQGNMTLDLLKDVIRKARNETSEFLIIEKFLELDDKKTEVYAQNWVGSTLLPPNISFREFQSLANIVNKVPNENSIENFLDLCLKLSFPVNLFTLLHVSMWSNNNFIYFIQSYVSKNENKLNVDLITLLKTSLPGNPELFSGLLPFLRRNKFMDILEYCIHSNPNLLNSIPDLNSDLLLKLLPRSRASYFAANIKLFKCSEQLTLVRWLLKGQQLEQLNQNFSEIENVLQNASDSELEKSEIIRELLHLAMANPIEPLFSGLLNFCIKNNMADHLDEFCGNMTSEVLFKISPELLLKLLTYKEKPNGKLLAAVIEKIENGDDDYILELLEKIIIQKEIQILEKLKEPLLVFFLNPVSSNMQKHKKSTNMLRELVLLYLTKPLSRSAAKKFFSMLISILPPNPNYQTIDMVNLLIDLIKSHNRKFKDKRTYNATLKTIGKWIQESGVVHQGDSSKEIEAI

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

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Unit-cell length a length_a	203.568 Å
Unit-cell length b length_b	203.568 Å
Unit-cell length c length_c	197.723 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	3.950 Å
Low-resolution limit resolution_low	49.300 Å
R factor r_factor	0.2140
R_work r_work	0.2120
R_free r_free	0.2610

Crystal structure of the Rif1 N-terminal domain (RIF1-NTD) from Saccharomyces cerevisiae

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

Telomere length regulator protein RIF1

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

5nvr__assembly_1__model_1

5nvr__assembly_1__model_1 | I(q)

5nvr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)

Crystal structure of the Rif1 N-terminal domain (RIF1-NTD) from Saccharomyces cerevisiae

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

Telomere length regulator protein RIF1

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

5nvr__assembly_1__model_1

5nvr__assembly_1__model_1 | I(q)

5nvr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)