SAXSdb — 3fma

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

Protein SMY2

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	Branchpoint-bridging protein × 1 （Q12186）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Branchpoint-bridging protein × 1 （Q12186）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Branchpoint-bridging protein × 1 （Q12186） water × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Branchpoint-bridging protein × 1 （Q12186） water × 1	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Branchpoint-bridging protein × 1 （Q12186） water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMY2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–100； UniProt 193–290 Author chain B； PDBConstruct 3–100； UniProt 193–290 Author chain C； PDBConstruct 3–100； UniProt 193–290 Author chain D； PDBConstruct 3–100； UniProt 193–290 Author chain E； PDBConstruct 3–100； UniProt 193–290

Branchpoint-bridging protein

OrganismNot specified

UniProt Q12186

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Protein SMY2 × 1 （P32909）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Protein SMY2 × 1 （P32909）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Protein SMY2 × 1 （P32909） water × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Protein SMY2 × 1 （P32909） water × 1	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Protein SMY2 × 1 （P32909） water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BBP_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–11； UniProt 440–450 Author chain M； PDBConstruct 1–11； UniProt 440–450 Author chain N； PDBConstruct 1–11； UniProt 440–450 Author chain O； PDBConstruct 1–11； UniProt 440–450 Author chain P； PDBConstruct 1–11； UniProt 440–450

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	3fma
Deposition date deposition_date	2008-12-19
Structure title title	Crystal structure of the GYF domain of Smy2 in complex with a proline-rich peptide from BBP/ScSF1
Keywords keywords	GYF domain, poly-proline binding, proline-rich peptide, domain swap, PRS, RAGNYA, PROTEIN BINDING; PROTEIN BINDING
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.

3fma__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3fma__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fma__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	15.38 Å
Rg (electron density)	14.39 Å
Total Rg	15.37 Å
Atom count	727
Residues	89
Excluded volume	13041 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fma__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fma__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3fma__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3fma__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3fma__assembly_5__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 (3)

Entity 1 Entity 1 polymer

Description description	Protein SMY2
Molecular weight formula_weight	11296.9 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	3609

GSNGMSQLPAPVSVESSWRYIDTQGQIHGPFTTQMMSQWYIGGYFASTLQISRLGSTPETLGINDIFITLGELMTKLEKYDTDPFTTFDKLHVQTTSSDS

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Branchpoint-bridging protein
Molecular weight formula_weight	982.1 kDa
Source method src_method	syn
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,M,N,O,P

SSIAPPPGLSG

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	3fmaA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	40 — GYF domain

Domain ID domain_id	3fmaB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	40 — GYF domain

Domain ID domain_id	3fmaC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	40 — GYF domain

Domain ID domain_id	3fmaD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	40 — GYF domain

Domain ID domain_id	3fmaE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	40 — GYF domain

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Unit-cell length a length_a	101.400 Å
Unit-cell length b length_b	101.400 Å
Unit-cell length c length_c	150.700 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	40

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	48.057 Å
R factor r_factor	0.2260
R_work r_work	0.2250
R_free r_free	0.2500

Crystal structure of the GYF domain of Smy2 in complex with a proline-rich peptide from BBP/ScSF1

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

Protein SMY2

State in the Current Structure

Other States of the Same Protein in the Database

Branchpoint-bridging protein

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

3fma__assembly_3__model_1

3fma__assembly_3__model_1 | I(q)

3fma__assembly_3__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 water

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)

Crystal structure of the GYF domain of Smy2 in complex with a proline-rich peptide from BBP/ScSF1

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

Protein SMY2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Branchpoint-bridging protein

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

3fma__assembly_3__model_1

3fma__assembly_3__model_1 | I(q)

3fma__assembly_3__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 water

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)