SAXSdb — 1b7f

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

PROTEIN (SXL-LETHAL PROTEIN)

Drosophila melanogaster

UniProt P19339

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–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 82–249	Fragment：2 RNP-DOMAINS Mutation：F166Y	;RNA (5'-R(PGPUPUPGPUPUPUPUPUPUPUPU)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；pH 7.0, VAPOR DIFFUSION, HANGING DROP	Resolution 2.60 Å R-free 0.294
2	Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain B； UniProt 82–249	Fragment：2 RNP-DOMAINS Mutation：F166Y	;RNA (5'-R(PGPUPUPGPUPUPUPUPUPUPUPU)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；pH 7.0, VAPOR DIFFUSION, HANGING DROP	Resolution 2.60 Å R-free 0.294

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 1B7F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1SXL RESONANCE ASSIGNMENTS AND SOLUTION STRUCTURE OF THE SECOND RNA-BINDING DOMAIN OF SEX-LETHAL DETERMINED BY MULTIDIMENSIONAL HETERONUCLEAR MAGNETIC RESONANCE SPECTROSCOPY Deposited 1994-07-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 199–294（96 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2SXL SEX-LETHAL RBD1, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-07-16	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 122–209（88 aa） Fragment：RNA-BINDING DOMAIN 1 (RBD1), RESIDUES 122 - 209	Mutation：F166Y	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；298 K	Resolution not provided
3SXL SEX-LETHAL RNA RECOGNITION DOMAINS 1 AND 2 FROM DROSOPHILA MELANOGASTER Deposited 1999-04-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 111–294（184 aa） Fragment：RNA BINDING DOMAINS 1 AND 2 (RESIDUES 112-294 OF FULL LENGTH)	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；pH 7.80	Resolution 2.70 Å R-free 0.264
3SXL SEX-LETHAL RNA RECOGNITION DOMAINS 1 AND 2 FROM DROSOPHILA MELANOGASTER Deposited 1999-04-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 111–294（184 aa） Fragment：RNA BINDING DOMAINS 1 AND 2 (RESIDUES 112-294 OF FULL LENGTH)	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；pH 7.80	Resolution 2.70 Å R-free 0.264
3SXL SEX-LETHAL RNA RECOGNITION DOMAINS 1 AND 2 FROM DROSOPHILA MELANOGASTER Deposited 1999-04-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 111–294（184 aa） Fragment：RNA BINDING DOMAINS 1 AND 2 (RESIDUES 112-294 OF FULL LENGTH)	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；pH 7.80	Resolution 2.70 Å R-free 0.264
4QQB Structural basis for the assembly of the SXL-UNR translation regulatory complex Deposited 2014-06-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain A 122–294（173 aa） Fragment：RRM1-RRM2, UNP residues 122-294	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M LiSO4, PEG3350 1-5 %, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.236
4QQB Structural basis for the assembly of the SXL-UNR translation regulatory complex Deposited 2014-06-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain B 122–294（173 aa） Fragment：RRM1-RRM2, UNP residues 122-294	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M LiSO4, PEG3350 1-5 %, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.236

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SXL_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–168； UniProt 82–249 Author chain B； PDBConstruct 1–168； UniProt 82–249

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	1b7f
Deposition date deposition_date	1999-01-23
Structure title title	SXL-LETHAL PROTEIN/RNA COMPLEX
Keywords keywords	;SPLICING REGULATION, RNP DOMAIN, RNA COMPLEX, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, RNA-BINDING PROTEIN-RNA COMPLEX ;; RNA-BINDING PROTEIN/RNA
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	30.21 Å
Radius of gyration Rg (electron density) rg_electron	30.10 Å
Forward intensity I(0) i0	41877400.00
Molecular weight molecular_weight	45330.0 kDa
Excluded volume excluded_volume	54449 Å³
Envelope volume envelope_volume	74722 Å³
Hydration-shell volume shell_volume	22069 Å³
Envelope diameter envelope_diameter	100.3 Å
Shell Rg shell_rg	35.18 Å
Envelope Rg envelope_rg	29.24 Å
Shape Rg shape_rg	30.08 Å
Total Rg total_rg	30.60 Å
Total atoms total_atoms	3152
Residues n_residues	358
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	97.5 Å
Rg (real space) rg_real	30.42 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	4.1880e+07
I(0) uncertainty (real space) i0_real_error	6.7800e+05
Rg (reciprocal space) rg_reciprocal	30.33 Å
I(0) (reciprocal space) i0_reciprocal	41870000.0000
Solution quality estimate total_estimate	0.8295
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	22.5 Å
Skewness Skewness skewness	0.349
Kurtosis Kurtosis kurtosis	-0.805
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6178000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.773; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.622; Smooth: 0.840

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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	;RNA (5'-R(PGPUPUPGPUPUPUPUPUPUPUPU)-3') ;
Molecular weight formula_weight	3707.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	P,Q
Atom count atom_count	3236

GUUGUUUUUUUU

Entity 2 Entity 2 polymer

Description description	PROTEIN (SXL-LETHAL PROTEIN)
Molecular weight formula_weight	18971.6 kDa
Mutation mutation	F166Y
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	84

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1b7fa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.1 — Canonical RBD

Domain ID domain_id	d1b7fa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.1 — Canonical RBD

Domain ID domain_id	d1b7fb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.1 — Canonical RBD

Domain ID domain_id	d1b7fb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.1 — Canonical RBD

CATH v4.4 (4 domains)

Domain ID domain_id	1b7fA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	1b7fA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	1b7fB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	1b7fB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

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8. Citations (1)

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Unit-cell length a length_a	77.900 Å
Unit-cell length b length_b	86.800 Å
Unit-cell length c length_c	160.400 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	16

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.2010
R_free r_free	0.2940

fit	/app/data/saxs_computation/b7/1b7f/1b7f.fit
pddf	/app/data/pr_computation/b7/1b7f/1b7f.pr.out
profile	/app/data/saxs_computation/b7/1b7f/1b7f.dat

SXL-LETHAL PROTEIN/RNA COMPLEX

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

PROTEIN (SXL-LETHAL PROTEIN)

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)