SAXSdb — 2l34

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

TYRO protein tyrosine kinase-binding protein

Homo sapiens

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 35–67 Chain B； UniProt 35–67	Fragment：UNP RESIDUES 35-67	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.8；303 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition：0.5 (dimer) mM [U-100% 13C; U-100% 15N; U-80% 2H] DAP12 transmembrane peptide-1, 20 mM sodium phosphate-2, 25 mM SDS-3, 250 mM Foscholine-14-4, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：0.5 (dimer) mM [U-100% 13C; U-100% 15N] DAP12 transmembrane peptide-5, 20 mM sodium phosphate-6, 25 mM [U-100% 2H] SDS-7, 250 mM [U-100% 2H] Foscholine-14-8, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：0.5 (monomer) mM [U-100% 15N; U-100% 2H] DAP12 transmembrane peptide-9, 0.5 (monomer) mM [U-100% 13C] DAP12 transmembrane peptide-10, 25 mM [U-100% 2H] SDS-11, 250 mM [U-100% 2H] Foscholine-14-12, 20 mM sodium phosphate-13, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：0.5 (dimer) mM [U-10% 13C] DAP12 transmembrane peptide-14, 25 mM [U-100% 2H] SDS-15, 250 mM [U-100% 2H] Foscholine-14-16, 20 mM sodium phosphate-17, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

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 2L34	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2L35 Structure of the DAP12-NKG2C transmembrane heterotrimer Deposited 2010-09-06	Different construct Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 35–67（33 aa） Chain B 35–66（32 aa） Fragment：UNP RESIDUES 35-66	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 0.5-1 mM [U-100% 13C; U-100% 15N; U-80% 2H] DAP12-NKG2C TM-1, 0.5-1 mM DAP12 TM-2, 25 mM SDS-3, 250 mM Foscholine-14-4, 20 mM sodium phosphate-5, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5-1 mM DAP12-NKG2C TM-6, 0.5-1 mM [U-100% 13C; U-100% 15N; U-80% 2H] DAP12 TM-7, 25 mM SDS-8, 250 mM Foscholine-14-9, 20 mM sodium phosphate-10, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5-1 mM [U-100% 13C; U-100% 15N] DAP12-NKG2C TM-11, 0.5-1 mM DAP12 TM-12, 25 mM [U-100% 2H] SDS-13, 250 mM [U-100% 2H] Foscholine-14-14, 20 mM sodium phosphate-15, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5-1 mM DAP12-NKG2C TM-16, 0.5-1 mM [U-100% 13C; U-100% 15N] DAP12 TM-17, 25 mM [U-100% 2H] SDS-18, 250 mM [U-100% 2H] Foscholine-14-19, 20 mM sodium phosphate-20, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5-1 mM [U-100% 15N; U-100% 2H] DAP12-NKG2C TM-21, 0.5-1 mM [U-10% 13C] DAP12 TM-22, 25 mM [U-100% 2H] SDS-23, 250 mM [U-100% 2H] Foscholine-14-24, 20 mM sodium phosphate-25, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5-1 mM [U-10% 13C] DAP12-NKG2C TM-26, 0.5-1 mM [U-100% 15N; U-90% 2H] DAP12 TM-27, 25 mM [U-100% 2H] SDS-28, 250 mM [U-100% 2H] Foscholine-14-29, 20 mM sodium phosphate-30, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
4WO1 Crystal structure of the DAP12 transmembrane domain in lipid cubic phase Deposited 2014-10-15	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 35–67（33 aa） Fragment：UNP residues 35-67 Chain D 35–67（33 aa） Fragment：UNP residues 35-67	Mutation：M21V Mutation：M21V	CA CALCIUM ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 3	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.07；293 K；0.1 M bis-tris propane chloride pH 6.07, 19.7 %w/v PEG 3350, 0.27 M calcium chloride	Resolution 2.14 Å R-free 0.296
4WO1 Crystal structure of the DAP12 transmembrane domain in lipid cubic phase Deposited 2014-10-15	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 35–67（33 aa） Fragment：UNP residues 35-67 Chain C 35–67（33 aa） Fragment：UNP residues 35-67	Mutation：M21V Mutation：M21V	OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 3	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.07；293 K；0.1 M bis-tris propane chloride pH 6.07, 19.7 %w/v PEG 3350, 0.27 M calcium chloride	Resolution 2.14 Å R-free 0.296
4WOL Crystal Structure of the DAP12 transmembrane domain in lipidic cubic phase Deposited 2014-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 35–67（33 aa） Fragment：UNP residues 35-67 Chain B 35–67（33 aa） Fragment：UNP residues 35-67 Chain C 35–67（33 aa） Fragment：UNP residues 35-67	Mutation：M21V Mutation：M21V Mutation：M21V	K POTASSIUM ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 4	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；12.4% w/v PEG 3350, 0.149 M potassium thiocyanate	Resolution 1.77 Å R-free 0.223
7Q5W The tandem SH2 domains of SYK with a bound TYROBP diphospho-ITAM peptide Deposited 2021-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain JJJ 88–107（20 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM Tris/BICINE, 10% PEG 20,000, 20% PEG 500 MME	Resolution 2.20 Å R-free 0.266
7Q5W The tandem SH2 domains of SYK with a bound TYROBP diphospho-ITAM peptide Deposited 2021-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain LLL 88–107（20 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM Tris/BICINE, 10% PEG 20,000, 20% PEG 500 MME	Resolution 2.20 Å R-free 0.266
7Q5W The tandem SH2 domains of SYK with a bound TYROBP diphospho-ITAM peptide Deposited 2021-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain KKK 88–107（20 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM Tris/BICINE, 10% PEG 20,000, 20% PEG 500 MME	Resolution 2.20 Å R-free 0.266
7Q5W The tandem SH2 domains of SYK with a bound TYROBP diphospho-ITAM peptide Deposited 2021-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain GGG 88–107（20 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM Tris/BICINE, 10% PEG 20,000, 20% PEG 500 MME	Resolution 2.20 Å R-free 0.266
7Q5W The tandem SH2 domains of SYK with a bound TYROBP diphospho-ITAM peptide Deposited 2021-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain III 88–107（20 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 1 P4G 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM Tris/BICINE, 10% PEG 20,000, 20% PEG 500 MME	Resolution 2.20 Å R-free 0.266
7Q5W The tandem SH2 domains of SYK with a bound TYROBP diphospho-ITAM peptide Deposited 2021-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain HHH 88–107（20 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM Tris/BICINE, 10% PEG 20,000, 20% PEG 500 MME	Resolution 2.20 Å R-free 0.266

4 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TYOBP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–33； UniProt 35–67 Author chain B； PDBConstruct 1–33； UniProt 35–67

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	2l34
Deposition date deposition_date	2010-09-06
Structure title title	Structure of the DAP12 transmembrane homodimer
Keywords keywords	Immunoreceptor, transmembrane assembly, DAP12, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	16.37 Å
Radius of gyration Rg (electron density) rg_electron	16.30 Å
Forward intensity I(0) i0	93195500.00
Molecular weight molecular_weight	98912.0 kDa
Excluded volume excluded_volume	131490 Å³
Envelope volume envelope_volume	17868 Å³
Hydration-shell volume shell_volume	9161 Å³
Envelope diameter envelope_diameter	66.6 Å
Shell Rg shell_rg	22.51 Å
Envelope Rg envelope_rg	20.08 Å
Shape Rg shape_rg	16.19 Å
Total Rg total_rg	17.00 Å
Total atoms total_atoms	14700
Residues n_residues	990
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	63.6 Å
Rg (real space) rg_real	16.92 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	9.3200e+07
I(0) uncertainty (real space) i0_real_error	1.3420e+06
Rg (reciprocal space) rg_reciprocal	16.87 Å
I(0) (reciprocal space) i0_reciprocal	93190000.0000
Solution quality estimate total_estimate	0.6245
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	13.1 Å
Skewness Skewness skewness	0.662
Kurtosis Kurtosis kurtosis	-0.313
Angular range angular_range	— – 0.4850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20820.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.035; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.019; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Description description	TYRO protein tyrosine kinase-binding protein
Molecular weight formula_weight	3331.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	14700

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/l3/2l34/2l34.fit
pddf	/app/data/pr_computation/l3/2l34/2l34.pr.out
profile	/app/data/saxs_computation/l3/2l34/2l34.dat

Structure of the DAP12 transmembrane homodimer

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

TYRO protein tyrosine kinase-binding 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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)