SAXSdb — 5nw5

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

Telomere length regulator protein RIF1

Saccharomyces cerevisiae S288c

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	DNA (60-MER) × 1 DNA (30-MER) × 1	Consistent with all polymers

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 5–1226； UniProt 100–1321 Author chain B； PDBConstruct 5–1226； UniProt 100–1321

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	5nw5
Deposition date deposition_date	2017-05-05
Structure title title	Crystal structure of the Rif1 N-terminal domain (RIF1-NTD) from Saccharomyces cerevisiae in complex with DNA
Keywords keywords	telomere maintenance, DNA double-strand break repair, irregular helical repeat, all-alpha fold, DNA binding protein; DNA BINDING 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.

5nw5__assembly_1__model_1

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

Download this curve (.dat)

5nw5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5nw5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	80.02 Å
Rg (electron density)	81.56 Å
Total Rg	81.21 Å
Atom count	37748
Residues	2230
Excluded volume	338130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5nw5__assembly_1__model_1`	tetrameric （4）	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 (3)

Entity 1 Entity 1 polymer

Description description	Telomere length regulator protein RIF1
Molecular weight formula_weight	140781.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	37748

GGGRELSASNSDNVSPVTKSVAFSDRIESSPIYRIPGSSPKPSPSSKPGKSILRNRLPSVRTVSDLSYNKLQYTQHKLHNGNIFTSPYKETRVNPRALEYWVSGEIHGLVDNESVSEFKEIIEGGLGILRQESEDYVARRFEVYATFNNIIPILTTKNVNEVDQKFNILIVNIESIIEICIPHLQIAQDTLLSSSEKKNPFVIRLYVQIVRFFSAIMSNFKIVKWLTKRPDLVNKLKVIYRWTTGALRNENSNKIIITAQVSFLRDEKFGTFFLSNEEIKPIISTFTEIMEINSHNLIYEKLLLIRGFLSKYPKLMIETVTSWLPGEVLPRIIIGDEIYSMKILITSIVVLLELLKKCLDFVDEHERIYQCIMLSPVCETIPEKFLSKLPLNSYDSANLDKVTIGHLLTQQIKNYIVVKNDNKIAMDLWLSMTGLLYDSGKRVYDLTSESNKVWFDLNNLCFINNHPKTRLMSIKVWRIITYCICTKISQKNQEGNKSLLSLLRTPFQMTLPYVNDPSAREGIIYHLLGVVYTAFTSNKNLSTDMFELFWDHLITPIYEDYVFKYDSIHLQNVLFTVLHLLIGGKNADVALERKYKKHIHPMSVIASEGVKLKDISSLPPQIIKREYDKIMKVVFQAVEVAISNVNLAHDLILTSLKHLPEDRKDQTHLESFSSLILKVTQNNKDTPIFRDFFGAVTSSFVYTFLDLFLRKNDSSLVNFNIQISKVGISQGNMTLDLLKDVIRKARNETSEFLIIEKFLELDDKKTEVYAQNWVGSTLLPPNISFREFQSLANIVNKVPNENSIENFLDLCLKLSFPVNLFTLLHVSMWSNNNFIYFIQSYVSKNENKLNVDLITLLKTSLPGNPELFSGLLPFLRRNKFMDILEYCIHSNPNLLNSIPDLNSDLLLKLLPRSRASYFAANIKLFKCSEQLTLVRWLLKGQQLEQLNQNFSEIENVLQNASDSELEKSEIIRELLHLAMANPIEPLFSGLLNFCIKNNMADHLDEFCGNMTSEVLFKISPELLLKLLTYKEKPNGKLLAAVIEKIENGDDDYILELLEKIIIQKEIQILEKLKEPLLVFFLNPVSSNMQKHKKSTNMLRELVLLYLTKPLSRSAAKKFFSMLISILPPNPNYQTIDMVNLLIDLIKSHNRKFKDKRTYNATLKTIGKWIQESGVVHQGDSSKEIEAIPDTKSMYIPCEGSENKLSNLQRKVDSQDIQVPATQGMKE

Source Source

Source organism organism	Saccharomyces cerevisiae S288c
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	DNA (60-MER)
Molecular weight formula_weight	9351.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Entity 3 Entity 3 polymer

Description description	DNA (30-MER)
Molecular weight formula_weight	9080.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

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Unit-cell length a length_a	92.140 Å
Unit-cell length b length_b	169.800 Å
Unit-cell length c length_c	390.160 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	6.502 Å
Low-resolution limit resolution_low	43.232 Å
R factor r_factor	0.2543
R_work r_work	0.2527
R_free r_free	0.2765

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

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

5nw5__assembly_1__model_1

5nw5__assembly_1__model_1 | I(q)

5nw5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

7. Citations (1)

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

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

5nw5__assembly_1__model_1

5nw5__assembly_1__model_1 | I(q)

5nw5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

7. Citations (1)