SAXSdb — 4qqb

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

Protein sex-lethal

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 Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 122–294	Fragment：RRM1-RRM2, UNP residues 122-294	msl2 mRNA × 1 Upstream of N-ras, isoform A × 1 （Q9VSK3）	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
2	Protein–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain B； UniProt 122–294	Fragment：RRM1-RRM2, UNP residues 122-294	msl2 mRNA × 1 Upstream of N-ras, isoform A × 1 （Q9VSK3）	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

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 4QQB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B7F SXL-LETHAL PROTEIN/RNA COMPLEX Deposited 1999-01-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 82–249（168 aa） Fragment：2 RNP-DOMAINS	Mutation：F166Y	No recorded non-water small molecule	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
1B7F SXL-LETHAL PROTEIN/RNA COMPLEX Deposited 1999-01-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 82–249（168 aa） Fragment：2 RNP-DOMAINS	Mutation：F166Y	No recorded non-water small molecule	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
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 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 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 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

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 4–176； UniProt 122–294 Author chain B； PDBConstruct 4–176； UniProt 122–294

Upstream of N-ras, isoform A

Drosophila melanogaster

UniProt Q9VSK3

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 Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain X； UniProt 185–252	Fragment：CSD1, UNP residues 185-252	msl2 mRNA × 1 Protein sex-lethal × 1 （P19339）	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
2	Protein–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain Y； UniProt 185–252	Fragment：CSD1, UNP residues 185-252	msl2 mRNA × 1 Protein sex-lethal × 1 （P19339）	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

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 4QQB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6Y4H Solution structure of cold-shock domain 7 and 8 of drosophila Upstream of N-Ras (Unr) Deposited 2020-02-21	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 756–922（167 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1 NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N] dCSD78, 150 mM sodium chloride, 20 mM sodium phosphate, 1 mM DTT, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N] dCSD78, 150 mM sodium chloride, 20 mM sodium phosphate, 1 mM DTT, 100% D2O \| 100% D2O	Resolution not provided
6Y6E drosophila Unr CSD456 Deposited 2020-02-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 424–677（254 aa）	Not recorded	EMC ETHYL MERCURY ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M tri-sodium citrate (pH 5.5), 20% PEG2000	Resolution 2.02 Å R-free 0.251
6Y6M solution structure of cold-shock domain 1 and 2 of drosophila Upstream of N-Ras (Unr) Deposited 2020-02-26	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 186–344（159 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 50 mM sodium chloride, 20 mM sodium phosphate, 10 mM DTT, 0.3 mM [U-99% 13C; U-99% 15N] protein, 0.36 mM RNA, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 50 mM sodium chloride, 20 mM sodium phosphate, 10 mM DTT, 0.3 mM [U-99% 13C; U-99% 15N] protein, 0.36 mM RNA, 100% D2O \| 100% D2O	Resolution not provided
6Y96 solution structure of cold-shock domain 9 of drosophila Upstream of N-Ras (Unr) Deposited 2020-03-06	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 899–990（92 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.24 mM [U-99% 13C; U-99% 15N] protein, 50 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.24 mM [U-99% 13C; U-99% 15N] protein, 50 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 100% D2O \| 100% D2O	Resolution not provided
7ZHH Complex structure of drosophila Unr CSD789 and a poly(A) RNA sequence Deposited 2022-04-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 756–990（235 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M Tris-Cl (pH 7.0) 0.2 M lithium sulfate 2 M ammonium sulfate	Resolution 1.60 Å R-free 0.210
7ZHR Complex structure of drosophila Unr CSD789 and pAbp RRM3 Deposited 2022-04-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 756–990（235 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M sodium formate 0.1 M bis-tris propane 20 % (w/v) PEG 3350	Resolution 2.99 Å R-free 0.315

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

View Construct and Data Evidence

UniProt name	Q9VSK3_DROME
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain X； PDBConstruct 5–72； UniProt 185–252 Author chain Y； PDBConstruct 5–72； UniProt 185–252

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	4qqb
Deposition date deposition_date	2014-06-27
Structure title title	Structural basis for the assembly of the SXL-UNR translation regulatory complex
Keywords keywords	;RNA binding domains, RNA recognition motif, RRM, cold shock domain, CSD, RNA binding, translation regulation, dosage compensation, TRANSCRIPTION-RNA complex, TRANLATION-RNA complex ;; TRANLATION/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	30.01 Å
Radius of gyration Rg (electron density) rg_electron	29.93 Å
Forward intensity I(0) i0	86967100.00
Molecular weight molecular_weight	65459.0 kDa
Excluded volume excluded_volume	78453 Å³
Envelope volume envelope_volume	106060 Å³
Hydration-shell volume shell_volume	30637 Å³
Envelope diameter envelope_diameter	110.3 Å
Shell Rg shell_rg	35.28 Å
Envelope Rg envelope_rg	29.97 Å
Shape Rg shape_rg	29.94 Å
Total Rg total_rg	30.36 Å
Total atoms total_atoms	4556
Residues n_residues	516
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	30.10 Å
Rg uncertainty (real space) rg_real_error	1.02 Å
I(0) (real space) i0_real	8.6970e+07
I(0) uncertainty (real space) i0_real_error	1.4920e+06
Rg (reciprocal space) rg_reciprocal	30.06 Å
I(0) (reciprocal space) i0_reciprocal	86960000.0000
Solution quality estimate total_estimate	0.8054
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.1 Å
Skewness Skewness skewness	0.396
Kurtosis Kurtosis kurtosis	-0.312
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19730000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.000

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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	msl2 mRNA
Molecular weight formula_weight	5712.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	P,C
Atom count atom_count	4556

UUUUUUUGAGCACGUGAA

Entity 2 Entity 2 polymer

Description description	Protein sex-lethal
Molecular weight formula_weight	19797.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GAMASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSFGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLAEEHGK

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

Entity 3 Entity 3 polymer

Description description	Upstream of N-ras, isoform A
Molecular weight formula_weight	8205.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,Y

GAMATRETGIIEKLLHSYGFIQCCERQARLFFHFSQFSGNIDHLKIGDPVEFEMTYDRRTGKPIASQVSKIA

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

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4qqbA01
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	4qqbA02
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	4qqbB01
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	4qqbB02
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	4qqbX01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	4qqbY01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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8. Citations (1)

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Unit-cell length a length_a	94.360 Å
Unit-cell length b length_b	110.970 Å
Unit-cell length c length_c	139.150 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	2.800 Å
Low-resolution limit resolution_low	19.930 Å
R factor r_factor	0.2001
R_work r_work	0.1982
R_free r_free	0.2356

fit	/app/data/saxs_computation/qq/4qqb/4qqb.fit
pddf	/app/data/pr_computation/qq/4qqb/4qqb.pr.out
profile	/app/data/saxs_computation/qq/4qqb/4qqb.dat

Structural basis for the assembly of the SXL-UNR translation regulatory complex

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

Protein sex-lethal

State in the Current Structure

Other States of the Same Protein in the Database

Upstream of N-ras, isoform A

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 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)