SAXSdb — 4f7z

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

Rap guanine nucleotide exchange factor 4

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–993	Fragment：SEE REMARK 999 Mutation：F435G	GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100 mM Bis-Tris propane, pH 7.5, 200 mM sodium chloride, 1.3 M ammonium sulfate, 6% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.282

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4F7Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2BYV Structure of the cAMP responsive exchange factor Epac2 in its auto- inhibited state Deposited 2005-08-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–993（993 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；100 MM BISTRISPROPANE7.5, 200 MM NANO3, 12% PEG 3350, pH 7.50	Resolution 2.70 Å R-free 0.297
4MGI Selective activation of Epac1 and Epac2 Deposited 2013-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 324–1011（688 aa） Fragment：UNP residues 324-1011	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.271
4MGI Selective activation of Epac1 and Epac2 Deposited 2013-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 324–1011（688 aa） Fragment：UNP residues 324-1011	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.271
4MGK Selective activation of Epac1 and Epac2 Deposited 2013-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 324–1011（688 aa） Fragment：UNP residues 324-1011	Mutation：K405Q	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.264
4MGK Selective activation of Epac1 and Epac2 Deposited 2013-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 324–1011（688 aa） Fragment：UNP residues 324-1011	Mutation：K405Q	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.264
4MGY Selective activation of Epac1 and Epac2 Deposited 2013-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 324–1011（688 aa） Fragment：UNP residues 324-1011	Mutation：K405Q	H07 (2S,4aR,6R,7R,7aR)-6-{6-amino-8-[(4-chlorophenyl)sulfanyl]-9H-purin-9-yl}-7-methoxytetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-2-ol 2-oxide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.60 Å R-free 0.270
4MGY Selective activation of Epac1 and Epac2 Deposited 2013-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 324–1011（688 aa） Fragment：UNP residues 324-1011	Mutation：K405Q	H07 (2S,4aR,6R,7R,7aR)-6-{6-amino-8-[(4-chlorophenyl)sulfanyl]-9H-purin-9-yl}-7-methoxytetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-2-ol 2-oxide × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.60 Å R-free 0.270
4MGZ Selective activation of Epac1 and Epac2 Deposited 2013-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 324–1011（688 aa） Fragment：UNP residues 324-1011	Not recorded	HR6 (2S,4aR,6R,7R,7aS)-6-[6-amino-8-(benzylsulfanyl)-9H-purin-9-yl]-2-sulfanyltetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol 2-oxide × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.00 Å R-free 0.264
4MGZ Selective activation of Epac1 and Epac2 Deposited 2013-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 324–1011（688 aa） Fragment：UNP residues 324-1011	Not recorded	HR6 (2S,4aR,6R,7R,7aS)-6-[6-amino-8-(benzylsulfanyl)-9H-purin-9-yl]-2-sulfanyltetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol 2-oxide × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.00 Å R-free 0.264
4MH0 Selective activation of Epac1 and Epac2 Deposited 2013-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 324–1011（688 aa） Fragment：UNP residues 324-1011	Not recorded	HR4 (2S,4aR,6R,7R,7aS)-6-{6-amino-8-[(4-fluorobenzyl)sulfanyl]-9H-purin-9-yl}-2-sulfanyltetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol 2-oxide × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.40 Å R-free 0.282
4MH0 Selective activation of Epac1 and Epac2 Deposited 2013-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 324–1011（688 aa） Fragment：UNP residues 324-1011	Not recorded	HR4 (2S,4aR,6R,7R,7aS)-6-{6-amino-8-[(4-fluorobenzyl)sulfanyl]-9H-purin-9-yl}-2-sulfanyltetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol 2-oxide × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.40 Å R-free 0.282

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPGF4_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–999； UniProt 1–993

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	4f7z
Deposition date deposition_date	2012-05-16
Structure title title	Conformational dynamics of exchange protein directly activated by cAMP
Keywords keywords	cyclic nucleotide, GEF, exchange factor, regulation, auto-inhibition, CDC25 homology domain, EXOCYTOSIS; EXOCYTOSIS
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	33.36 Å
Radius of gyration Rg (electron density) rg_electron	32.33 Å
Forward intensity I(0) i0	186342000.00
Molecular weight molecular_weight	108900.0 kDa
Excluded volume excluded_volume	136510 Å³
Envelope volume envelope_volume	182390 Å³
Hydration-shell volume shell_volume	46026 Å³
Envelope diameter envelope_diameter	108.8 Å
Shell Rg shell_rg	40.06 Å
Envelope Rg envelope_rg	31.95 Å
Shape Rg shape_rg	32.33 Å
Total Rg total_rg	32.98 Å
Total atoms total_atoms	7649
Residues n_residues	946
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	100.9 Å
Rg (real space) rg_real	33.19 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	1.8630e+08
I(0) uncertainty (real space) i0_real_error	3.0280e+06
Rg (reciprocal space) rg_reciprocal	33.30 Å
I(0) (reciprocal space) i0_reciprocal	186400000.0000
Solution quality estimate total_estimate	0.9088
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.1 Å
Skewness Skewness skewness	0.066
Kurtosis Kurtosis kurtosis	-0.582
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25210000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.948

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Rap guanine nucleotide exchange factor 4
Molecular weight formula_weight	114060.4 kDa
Mutation mutation	F435G
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	7666

GSPGIPMVAAHAAHSQSSAEWIACLDKRPLERSSEDVDIIFTRLKGVKAFEKFHPNLLRQICLCGYYENLEKGITLFRQGDIGTNWYAVLAGSLDVKVSETSSHQDAVTICTLGIGTAFGESILDNTPRHATIVTRESSELLRIEQEDFKALWEKYRQYMAGLLAPPYGVMETGSNNDRIPDKENVPSEKILRAGKILRIAILSRAPHMIRDRKYHLKTYRQCCVGTELVDWMIQQTSCVHSRTQAVGMWQVLLEDGVLNHVDQERHFQDKYLFYRFLDDEREDAPLPTEEEKKECDEELQDTMLLLSQMGPDAHMRMILRKPPGQRTVDDLEIIYDELLHIKALSHLSTTVKRELAGVLIFESHAKGGTVLFNQGEEGTSWYIILKGSVNVVIYGKGVVCTLHEGDDFGKLALVNDAPRAASIVLREDNCHFLRVDKEDGNRILRDVEANTVRLKEHDQDVLVLEKVPAGNRAANQGNSQPQQKYTVMSGTPEKILEHFLETIRLEPSLNEATDSVLNDFVMMHCVFMPNTQLCPALVAHYHAQPSQGTEQERMDYALNNKRRVIRLVLQWAAMYGDLLQEDDVAMAFLEEFYVSVSDDARMMAAFKEQLPELEKIVKQISEDAKAPQKKHKVLLQQFNTGDERAQKRQPIRGSDEVLFKVYCIDHTYTTIRVPVAASVKEVISAVADKLGSGEGLIIVKMNSGGEKVVLKSNDVSVFTTLTINGRLFACPREQFDSLTPLPEQEGPTTGTVGTFELMSSKDLAYQMTTYDWELFNCVHELELIYHTFGRHNFKKTTANLDLFLRRFNEIQFWVVTEVCLCSQLSKRVQLLKKFIKIAAHCKEYKNLNSFFAIVMGLSNVAVSRLALTWEKLPSKFKKFYAEFESLMDPSRNHRAYRLTAAKLEPPLIPFMPLLIKDMTFTHEGNKTFIDNLVNFEKMRMIANTARTVRYYRSQPFNPDAAQANKNHQDVRSYVRQLNVIDNQRTLSQMSHRLEPRRP

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	17

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4f7zA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	4f7zA02
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	4f7zA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	4f7zA04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	870 — Son of sevenless (SoS) protein; Chain S, domain 1
Homologous superfamily homologous superfamily	10 — Son of sevenless (SoS) protein Chain: S domain 1

Domain ID domain_id	4f7zA05
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	4f7zA06
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	840 — Son of Sevenless (SoS) protein; Chain S, domain 2
Homologous superfamily homologous superfamily	10 — Ras guanine-nucleotide exchange factors catalytic domain

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8. Citations (1)

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Unit-cell length a length_a	69.720 Å
Unit-cell length b length_b	95.350 Å
Unit-cell length c length_c	181.840 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	2.600 Å
Low-resolution limit resolution_low	45.460 Å
R factor r_factor	0.2220
R_work r_work	0.2220
R_free r_free	0.2820

fit	/app/data/saxs_computation/f7/4f7z/4f7z.fit
pddf	/app/data/pr_computation/f7/4f7z/4f7z.pr.out
profile	/app/data/saxs_computation/f7/4f7z/4f7z.dat

Conformational dynamics of exchange protein directly activated by cAMP

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

Rap guanine nucleotide exchange factor 4

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction