SAXSdb — 4bjt

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

DNA-BINDING PROTEIN RAP1

SACCHAROMYCES CEREVISIAE S288C

UniProt P11938

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	TELOMERE LENGTH REGULATOR PROTEIN RIF1 × 1 （P29539） 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	TELOMERE LENGTH REGULATOR PROTEIN RIF1 × 1 （P29539） 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	TELOMERE LENGTH REGULATOR PROTEIN RIF1 × 1 （P29539） 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAP1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–202； UniProt 627–827 Author chain B； PDBConstruct 2–202； UniProt 627–827 Author chain C； PDBConstruct 2–202； UniProt 627–827

TELOMERE LENGTH REGULATOR PROTEIN RIF1

OrganismNot specified

UniProt P29539

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA-BINDING PROTEIN RAP1 × 1 （P11938） 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA-BINDING PROTEIN RAP1 × 1 （P11938） 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	DNA-BINDING PROTEIN RAP1 × 1 （P11938） 1,2-ETHANEDIOL × 1 water × 2	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	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–20； UniProt 1752–1771 Author chain E； PDBConstruct 1–20； UniProt 1752–1771 Author chain F； PDBConstruct 1–20； UniProt 1752–1771

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	4bjt
Deposition date deposition_date	2013-04-19
Structure title title	Crystal structure of the Rap1 C-terminal domain (Rap1-RCT) in complex with the Rap1 binding module of Rif1 (Rif1-RBM)
Keywords keywords	TRANSCRIPTION, GENOME STABILITY, TELOMERE ASSOCIATED PROTEINS; TRANSCRIPTION
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.

4bjt__assembly_1__model_1

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

Download this curve (.dat)

4bjt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4bjt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.18 Å
Rg (electron density)	15.86 Å
Total Rg	16.93 Å
Atom count	2576
Residues	159
Excluded volume	23243 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4bjt__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4bjt__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4bjt__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Description description	DNA-BINDING PROTEIN RAP1
Molecular weight formula_weight	23249.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	8538

GASNSYAIPENELLDEDTMNFISSLKNDLSNISNSLPFEYPHEIAEAIRSDFSNEDIYDNIDPDTISFPPKIATTDLFLPLFFHFGSTRQFMDKLHEVISGDYEPSQAEKLVQDLCDETGIRKNFSTSILTCLSGDLMVFPRYFLNMFKDNVNPPPNVPGIWTHDDDESLKSNDQEQIRKLVKKHGTGRMEMRKRFFEKDLL

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	TELOMERE LENGTH REGULATOR PROTEIN RIF1
Molecular weight formula_weight	2286.7 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

ADISVLPEIRIPIFNSLKMQ

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	646

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4bjtA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1480 —

Domain ID domain_id	4bjtA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	2170 —

Domain ID domain_id	4bjtB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1480 —

Domain ID domain_id	4bjtB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	2170 —

Domain ID domain_id	4bjtC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1480 —

Domain ID domain_id	4bjtC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	2170 —

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Unit-cell length a length_a	164.010 Å
Unit-cell length b length_b	88.900 Å
Unit-cell length c length_c	57.580 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.09 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.610 Å
Low-resolution limit resolution_low	47.160 Å
R factor r_factor	0.1673
R_work r_work	0.1664
R_free r_free	0.1849

Crystal structure of the Rap1 C-terminal domain (Rap1-RCT) in complex with the Rap1 binding module of Rif1 (Rif1-RBM)

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

DNA-BINDING PROTEIN RAP1

State in the Current Structure

Other States of the Same Protein in the Database

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

4bjt__assembly_1__model_1

4bjt__assembly_1__model_1 | I(q)

4bjt__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of the Rap1 C-terminal domain (Rap1-RCT) in complex with the Rap1 binding module of Rif1 (Rif1-RBM)

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

DNA-BINDING PROTEIN RAP1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

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

4bjt__assembly_1__model_1

4bjt__assembly_1__model_1 | I(q)

4bjt__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)