SAXSdb — 4dke

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

Interleukin-34

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	Other combination Heteromer Protein × 6 其他Polymer 2 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 21–193 Chain B； UniProt 21–193	Fragment：active core	FAb1.1 Heavy Chain × 2 FAb1.1 Light Chain × 2 ;alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M Ammonium phosphate monobasic, 0.1 M Tris pH 8.5, 50% v/v (+/-)-2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.00 Å R-free 0.265
2	Other combination Heteromer Protein × 6 其他Polymer 2 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 21–193 Chain B； UniProt 21–193	Fragment：active core	FAb1.1 Heavy Chain × 2 FAb1.1 Light Chain × 2 ;alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M Ammonium phosphate monobasic, 0.1 M Tris pH 8.5, 50% v/v (+/-)-2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.00 Å R-free 0.265

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 4DKE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4DKC Crystal Structure of Human Interleukin-34 Deposited 2012-02-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 21–193（173 aa） Chain B 21–193（173 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 10% w/v Polyethylene glycol 6,000, 5% v/v (+/-)-2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.85 Å R-free 0.203
4DKD Crystal Structure of Human Interleukin-34 Bound to Human CSF-1R Deposited 2012-02-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 21–193（173 aa） Fragment：active core, UNP residues 21-193 Chain B 21–193（173 aa） Fragment：active core, UNP residues 21-193	Not recorded	BMA beta-D-mannopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1M Calcium acetate, 0.1M Mes pH 6.0, 15% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.00 Å R-free 0.287
4DKF Crystal Structure of Human Interleukin-34 Bound to FAb2 Deposited 2012-02-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 21–193（173 aa） Fragment：active core Chain B 21–193（173 aa） Fragment：active core	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3,350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.61 Å R-free 0.256
4DKF Crystal Structure of Human Interleukin-34 Bound to FAb2 Deposited 2012-02-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 21–193（173 aa） Fragment：active core Chain B 21–193（173 aa） Fragment：active core	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3,350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.61 Å R-free 0.256

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

View Construct and Data Evidence

UniProt name	IL34_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–176； UniProt 21–193 Author chain B； PDBConstruct 4–176； UniProt 21–193

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	4dke
Deposition date deposition_date	2012-02-03
Structure title title	Crystal Structure of Human Interleukin-34 Bound to FAb1.1
Keywords keywords	dimeric four-helix bundle cytokine, IgG, glycosylation, CYTOKINE-IMMUNE SYSTEM complex; CYTOKINE/IMMUNE SYSTEM
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	44.09 Å
Radius of gyration Rg (electron density) rg_electron	44.78 Å
Forward intensity I(0) i0	248958000.00
Molecular weight molecular_weight	128720.0 kDa
Excluded volume excluded_volume	161250 Å³
Envelope volume envelope_volume	221790 Å³
Hydration-shell volume shell_volume	45983 Å³
Envelope diameter envelope_diameter	173.2 Å
Shell Rg shell_rg	42.46 Å
Envelope Rg envelope_rg	45.44 Å
Shape Rg shape_rg	44.74 Å
Total Rg total_rg	44.81 Å
Total atoms total_atoms	9059
Residues n_residues	1138
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	160.1 Å
Rg (real space) rg_real	44.82 Å
Rg uncertainty (real space) rg_real_error	2.36 Å
I(0) (real space) i0_real	2.4900e+08
I(0) uncertainty (real space) i0_real_error	5.0430e+06
Rg (reciprocal space) rg_reciprocal	44.09 Å
I(0) (reciprocal space) i0_reciprocal	248700000.0000
Solution quality estimate total_estimate	0.7508
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.0 Å
Skewness Skewness skewness	0.733
Kurtosis Kurtosis kurtosis	0.137
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23000000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.604; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.563; Smooth: 0.383

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Interleukin-34
Molecular weight formula_weight	21860.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9109

AGSNEPLEMWPLTQNEECTVTGFLRDKLQYRSRLQYMKHYFPINYKISVPYEGVFRIANVTRLQRAQVSERELRYLWVLVSLSATESVQDVLLEGHPSWKYLQEVETLLLNVQQGLTDVEVSPKVESVLSLLNAPGPNLKLVRPKALLDNCFRVMELLYCSCCKQSSVLNWQDCEVGNSGNSDYKDDDDK

来源 Source

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	FAb1.1 Heavy Chain
Molecular weight formula_weight	24433.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,I

EVQLVESGGGLVQPGGSLRLSCAASGFTFSSTWIHWVRQAPGKGLEWVARISPYYYYSDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARGLGKGSKRGAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

来源 Source

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	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	FAb1.1 Light Chain
Molecular weight formula_weight	23396.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,M

DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSFYFPNTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

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	Cricetulus griseus

Entity 4 Entity 4 branched

Description description	;alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 branched

Description description	;beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	50

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7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	4dkeA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	80 — Interleukin-34

Domain ID domain_id	4dkeB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	80 — Interleukin-34

Domain ID domain_id	4dkeH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4dkeH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4dkeI01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4dkeI02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4dkeL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4dkeL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4dkeM01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4dkeM02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	105.549 Å
Unit-cell length b length_b	122.465 Å
Unit-cell length c length_c	149.155 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	3.000 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2325
R_work r_work	0.2308
R_free r_free	0.2646

fit	/app/data/saxs_computation/dk/4dke/4dke.fit
pddf	/app/data/pr_computation/dk/4dke/4dke.pr.out
profile	/app/data/saxs_computation/dk/4dke/4dke.dat

Crystal Structure of Human Interleukin-34 Bound to FAb1.1

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

Interleukin-34

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)