SAXSdb — 4bj6

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

RAP1-INTERACTING FACTOR 2

SACCHAROMYCES CEREVISIAE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	DNA-BINDING PROTEIN RAP1 × 1 （P11938） SULFATE ION × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	DNA-BINDING PROTEIN RAP1 × 1 （P11938） SULFATE ION × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIF2_YEAST
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain A； PDBConstruct 5–365； UniProt 35–395 Author chain B； PDBConstruct 5–365； UniProt 35–395 Author chain D； PDBConstruct 1–13； UniProt 36–48 Author chain F； PDBConstruct 1–13； UniProt 36–48

DNA-BINDING PROTEIN RAP1

SACCHAROMYCES CEREVISIAE

UniProt P11938

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	RAP1-INTERACTING FACTOR 2 × 1 （Q06208） RAP1-INTERACTING FACTOR 2 × 1 （Q06208） SULFATE ION × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	RAP1-INTERACTING FACTOR 2 × 1 （Q06208） RAP1-INTERACTING FACTOR 2 × 1 （Q06208） SULFATE ION × 5	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	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–202； UniProt 627–827 Author chain E； PDBConstruct 2–202； UniProt 627–827

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	4bj6
Deposition date deposition_date	2013-04-16
Structure title title	Crystal structure Rif2 in complex with the C-terminal domain of Rap1 (Rap1-RCT)
Keywords keywords	TRANSCRIPTION, GENOME STABILITY, TELOMERE ASSOCIATED PROTEINS, AAA+ FOLD; 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.

4bj6__assembly_1__model_1

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

Download this curve (.dat)

4bj6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4bj6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.68 Å
Rg (electron density)	25.47 Å
Total Rg	26.42 Å
Atom count	3668
Residues	454
Excluded volume	65607 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4bj6__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4bj6__assembly_2__model_1`	trimeric （3）	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	RAP1-INTERACTING FACTOR 2
Molecular weight formula_weight	42145.8 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	7370

GGGRNFTVLRKLNLVPIKKSVSSPKVCKPSPVKERVDHVFYQKFKSMALQELGTNYLSISYVPSLSKFLSKNLRSMKNCIVFFDKVEHIHQYAGIDRAVSETLSLVDINVVIIEMNDYLMKEGIQSSKSKECIESMGQASYSGQLDFEASEKPSNHTSDLMMMVMRKINNDESIDHIVYFKFEQLDKLSTSTIIEPSKLTEFINVLSVLEKSNNIAFKVLIYSNNVSISSLLSTSLKKKLNTKYTVFEMPILTCAQEQEYLKKMIKFTFDSGSKLLQSYNSLVTCQLNNKESNLAIFFEFLKVFPHPFTYLFNAYTEIIVQSRTFDELLDKIRNRLTIKNYPHSAYNFKKNQRLPLKLTRKVHDR

Source Source

Source organism organism	SACCHAROMYCES CEREVISIAE
Common name common_name	;BAKER'S YEAST ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	TRICHOPLUSIA NI

Entity 2 Entity 2 polymer

Description description	DNA-BINDING PROTEIN RAP1
Molecular weight formula_weight	23249.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GASNSYAIPENELLDEDTMNFISSLKNDLSNISNSLPFEYPHEIAEAIRSDFSNEDIYDNIDPDTISFPPKIATTDLFLPLFFHFGSTRQFMDKLHEVISGDYEPSQAEKLVQDLCDETGIRKNFSTSILTCLSGDLMVFPRYFLNMFKDNVNPPPNVPGIWTHDDDESLKSNDQEQIRKLVKKHGTGRMEMRKRFFEKDLL

Source Source

Source organism organism	SACCHAROMYCES CEREVISIAE
Common name common_name	;BAKER'S YEAST ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	TRICHOPLUSIA NI

Entity 3 Entity 3 polymer

Description description	RAP1-INTERACTING FACTOR 2
Molecular weight formula_weight	1544.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

FTVLRKLNLVPIK

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	10

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4bj6A01
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	1650 —

Domain ID domain_id	4bj6A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12060 —

Domain ID domain_id	4bj6B01
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	1650 —

Domain ID domain_id	4bj6B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12060 —

Domain ID domain_id	4bj6C01
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	4bj6C02
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	4bj6E01
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	4bj6E02
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	108.250 Å
Unit-cell length b length_b	112.680 Å
Unit-cell length c length_c	140.790 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	3.260 Å
Low-resolution limit resolution_low	48.790 Å
R factor r_factor	0.1731
R_work r_work	0.1719
R_free r_free	0.1953

Crystal structure Rif2 in complex with the C-terminal domain of Rap1 (Rap1-RCT)

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

RAP1-INTERACTING FACTOR 2

State in the Current Structure

Other States of the Same Protein in the Database

DNA-BINDING PROTEIN RAP1

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

4bj6__assembly_1__model_1

4bj6__assembly_1__model_1 | I(q)

4bj6__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure Rif2 in complex with the C-terminal domain of Rap1 (Rap1-RCT)

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

RAP1-INTERACTING FACTOR 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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4bj6__assembly_1__model_1

4bj6__assembly_1__model_1 | I(q)

4bj6__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)