4bgd

Crystal structure of Brr2 in complex with the Jab1/MPN domain of Prp8

Method: X-RAY DIFFRACTION

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

PRE-MRNA-SPLICING HELICASE BRR2

SACCHAROMYCES CEREVISIAE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	PRE-MRNA-SPLICING FACTOR 8 × 1 （P33334） ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BRR2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1722； UniProt 442–2163

PRE-MRNA-SPLICING FACTOR 8

SACCHAROMYCES CEREVISIAE

UniProt P33334

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	PRE-MRNA-SPLICING HELICASE BRR2 × 1 （P32639） ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRP8_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–248； UniProt 2148–2395

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	4bgd
Deposition date deposition_date	2013-03-25
Structure title title	Crystal structure of Brr2 in complex with the Jab1/MPN domain of Prp8
Keywords keywords	TRANSCRIPTION, SPLICEOSOME, RNA HELICASE, U5 SNRNP, RETINITIS PIGMENTOSA; 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.

4bgd__assembly_1__model_1

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

Download this curve (.dat)

4bgd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4bgd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.22 Å
Rg (electron density)	43.62 Å
Total Rg	43.89 Å
Atom count	15718
Residues	1955
Excluded volume	281490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4bgd__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	PRE-MRNA-SPLICING HELICASE BRR2
Molecular weight formula_weight	195729.5 kDa
EC 编号 ec_number	3.6.4.13
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	15738

TVTKVSLPEGSFKRVKPQYDEIHIPAPSKPVIDYELKEITSLPDWCQEAFPSSETTSLNPIQSKVFHAAFEGDSNMLICAPTGSGKTNIALLTVLKALSHHYNPKTKKLNLSAFKIVYIAPLKALVQEQVREFQRRLAFLGIKVAELTGDSRLSRKQIDETQVLVSTPEKWDITTRNSNNLAIVELVRLLIIDEIHLLHDDRGPVLESIVARTFWASKYGQEYPRIIGLSATLPNYEDVGRFLRVPKEGLFYFDSSFRPCPLSQQFCGIKERNSLKKLKAMNDACYEKVLESINEGNQIIVFVHSRKETSRTATWLKNKFAEENITHKLTKNDAGSKQILKTEAANVLDPSLRKLIESGIGTHHAGLTRSDRSLSEDLFADGLLQVLVCTATLAWGVNLPAHTVIIKGTDVYSPEKGSWEQLSPQDVLQMLGRAGRPRYDTFGEGIIITDQSNVQYYLSVLNQQLPIESQFVSKLVDNLNAEVVAGNIKCRNDAVNWLAYTYLYVRMLASPMLYKVPDISSDGQLKKFRESLVHSALCILKEQELVLYDAENDVIEATDLGNIASSFYINHASMDVYNRELDEHTTQIDLFRIFSMSEEFKYVSVRYEEKRELKQLLEKAPIPIREDIDDPLAKVNVLLQSYFSQLKFEGFALNSDIVFIHQNAGRLLRAMFEICLKRGWGHPTRMLLNLCKSATTKMWPTNCPLRQFKTCPVEVIKRLEASTVPWGDYLQLETPAEVGRAIRSEKYGKQVYDLLKRFPKMSVTCNAQPITRSVMRFNIEIIADWIWDMNVHGSLEPFLLMLEDTDGDSILYYDVLFITPDIVGHEFTLSFTYELKQHNQNNLPPNFFLTLISENWWHSEFEIPVSFNGFKLPKKFPPPTPLLENISISTSELGNDDFSEVFEFKTFNKIQSQVFESLYNSNDSVFVGSGKGTGKTAMAELALLNHWRQNKGRAVYINPSGEKIDFLLSDWNKRFSHLAGGKIINKLGNDPSLNLKLLAKSHVLLATPVQFELLSRRWRQRKNIQSLELMIYDDAHEISQGVYGAVYETLISRMIFIATQLEKKIRFVCLSNCLANARDFGEWAGMTKSNIYNFSPSERIEPLEINIQSFKDVEHISFNFSMLQMAFEASAAAAGNRNSSSVFLPSRKDCMEVASAFMKFSKAIEWDMLNVEEEQIVPYIEKLTDGHLRAPLKHGVGILYKGMASNDERIVKRLYEYGAVSVLLISKDCSAFACKTDEVIILGTNLYDGAEHKYMPYTINELLEMVGLASGNDSMAGKVLILTSHNMKAYYKKFLIEPLPTESYLQYIIHDTLNNEIANSIIQSKQDCVDWFTYSYFYRRIHVNPSYYGVRDTSPHGISVFLSNLVETCLNDLVESSFIEIDDTEAEVTAEVNGGDDEATEIISTLSNGLIASHYGVSFFTIQSFVSSLSNTSTLKNMLYVLSTAVEFESVPLRKGDRALLVKLSKRLPLRFPEHTSSGSVSFKVFLLLQAYFSRLELPVDFQNDLKDILEKVVPLINVVVDILSANGYLNATTAMDLAQMLIQGVWDVDNPLRQIPHFNNKILEKCKEINVETVYDIMALEDEERDEILTLTDSQLAQVAAFVNNYPNVELTYSLNNSDSLISGVKQKITIQLTRDVEPENLQVTSEKYPFDKLESWWLVLGEVSKKELYAIKKVTLNKETQQYELEFDTPTSGKHNLTIWCVCDSYLDADKELSFEINVK

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	SACCHAROMYCES CEREVISIAE

Entity 2 Entity 2 polymer

Description description	PRE-MRNA-SPLICING FACTOR 8
Molecular weight formula_weight	28180.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

SKNEWRKSAIANTLLYLRLKNIYVSADDFVEEQNVYVLPKNLLKKFIEISDVKIQVAAFIYGMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDIGDLPDTEGLELLGWIHTQTEELKFMAASEVATHSKLFADKKRDCIDISIFSTPGSVSLSAYNLTDEGYQWGEENKDIMNVLSEGFEPTFSTHAQLLLSDRITGNFIIPSGNVWNYTFMGTAFNQEGDYNFKYGIPLEFYNEMHRPVHFLQF

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	SACCHAROMYCES CEREVISIAE

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
Molecular weight formula_weight	398.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	15

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4bgdc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.3 — JAB1/MPN domain
Family Family family	c.97.3.0 — automated matches

CATH v4.4 (13 domains)

Domain ID domain_id	4bgdA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4bgdA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4bgdA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	4bgdA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3380 — Sec63 N-terminal domain-like fold
Homologous superfamily homologous superfamily	10 — Sec63 N-terminal domain-like domain

Domain ID domain_id	4bgdA05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	4bgdA06
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

Domain ID domain_id	4bgdA07
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4bgdA08
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4bgdA09
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	4bgdA10
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3380 — Sec63 N-terminal domain-like fold
Homologous superfamily homologous superfamily	10 — Sec63 N-terminal domain-like domain

Domain ID domain_id	4bgdA11
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	4bgdA12
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

Domain ID domain_id	4bgdC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

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Unit-cell length a length_a	107.640 Å
Unit-cell length b length_b	178.640 Å
Unit-cell length c length_c	180.400 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	92.370 Å
R factor r_factor	0.2166
R_work r_work	0.2137
R_free r_free	0.2699

Crystal structure of Brr2 in complex with the Jab1/MPN domain of Prp8

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

PRE-MRNA-SPLICING HELICASE BRR2

State in the Current Structure

Other States of the Same Protein in the Database

PRE-MRNA-SPLICING FACTOR 8

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

4bgd__assembly_1__model_1

4bgd__assembly_1__model_1 | I(q)

4bgd__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (1 domains)

CATH v4.4 (13 domains)

7. Citations (1)

Crystal structure of Brr2 in complex with the Jab1/MPN domain of Prp8

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

PRE-MRNA-SPLICING HELICASE BRR2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PRE-MRNA-SPLICING FACTOR 8

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

4bgd__assembly_1__model_1

4bgd__assembly_1__model_1 | I(q)

4bgd__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (1 domains)

CATH v4.4 (13 domains)

7. Citations (1)