SAXSdb — 6gny

▼

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

Membrane-anchored junction 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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–106 Chain C； UniProt 1–106	Not recorded	Telomere repeats-binding bouquet formation protein 2 × 2 （Q8NHR7） TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.12M 1,6-Hexanediol; 0.12M 1-Butanol; 0.12M 1,2-Propanediol (racemic); 0.12M 2-Propanol; 0.12M 1,4-Butanediol; 0.12M 1,3-Propanediol; 39.1 mM bicine pH 5.03; 60.9 mM Trizma pH 10.83; 18.3% w/v PEG 1000; 18.3% w/v PEG 3350; 18.3% v/v MPD	Resolution 1.85 Å R-free 0.207

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 6GNY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6GNX Crystal structure of the MAJIN-TERB2 heterotetrameric complex - selenomethionine derivative Deposited 2018-06-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–112（112 aa） Chain C 1–112（112 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12M 1,6-Hexanediol; 0.12M 1-Butanol; 0.12M 1,2-Propanediol (racemic); 0.12M 2-Propanol; 0.12M 1,4-Butanediol; 0.12M 1,3-Propanediol, 55.5 mM MES pH 3.11, 44.5 mM imidazole pH 10.23; 12.5% w/v PEG 1000; 12.5% w/v PEG 3350; 12.5% v/v MPD	Resolution 2.90 Å R-free 0.304
6J08 Crystal structure of human MAJIN and TERB2 Deposited 2018-12-21	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 A 2–109（108 aa） Fragment：NTD domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.8；291 K；100 mM HEPES pH 6.8, 0.2 M Potassium thiocyanate, 22% (w/v) Polyethylene glycol 3350, 25% (v/v) Glycerol	Resolution 2.90 Å R-free 0.262
6J08 Crystal structure of human MAJIN and TERB2 Deposited 2018-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–109（108 aa） Fragment：NTD domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.8；291 K；100 mM HEPES pH 6.8, 0.2 M Potassium thiocyanate, 22% (w/v) Polyethylene glycol 3350, 25% (v/v) Glycerol	Resolution 2.90 Å R-free 0.262
6J08 Crystal structure of human MAJIN and TERB2 Deposited 2018-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–109（108 aa） Fragment：NTD domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.8；291 K；100 mM HEPES pH 6.8, 0.2 M Potassium thiocyanate, 22% (w/v) Polyethylene glycol 3350, 25% (v/v) Glycerol	Resolution 2.90 Å R-free 0.262

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

View Construct and Data Evidence

UniProt name	MAJIN_HUMAN
Isoform	Q3KP22-3
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–108； UniProt 1–106 Author chain C； PDBConstruct 3–108； UniProt 1–106

Telomere repeats-binding bouquet formation protein 2

Homo sapiens

UniProt Q8NHR7

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 168–207 Chain D； UniProt 168–207	Not recorded	Membrane-anchored junction protein × 2 （Q3KP22） TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.12M 1,6-Hexanediol; 0.12M 1-Butanol; 0.12M 1,2-Propanediol (racemic); 0.12M 2-Propanol; 0.12M 1,4-Butanediol; 0.12M 1,3-Propanediol; 39.1 mM bicine pH 5.03; 60.9 mM Trizma pH 10.83; 18.3% w/v PEG 1000; 18.3% w/v PEG 3350; 18.3% v/v MPD	Resolution 1.85 Å R-free 0.207

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 6GNY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6GNX Crystal structure of the MAJIN-TERB2 heterotetrameric complex - selenomethionine derivative Deposited 2018-06-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 169–220（52 aa） Chain D 169–220（52 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12M 1,6-Hexanediol; 0.12M 1-Butanol; 0.12M 1,2-Propanediol (racemic); 0.12M 2-Propanol; 0.12M 1,4-Butanediol; 0.12M 1,3-Propanediol, 55.5 mM MES pH 3.11, 44.5 mM imidazole pH 10.23; 12.5% w/v PEG 1000; 12.5% w/v PEG 3350; 12.5% v/v MPD	Resolution 2.90 Å R-free 0.304
6J07 Crystal structure of human TERB2 and TERB1 Deposited 2018-12-21	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 A 4–110（107 aa） Fragment：NTD domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 9；291 K；0.1 M Bicine pH 9.0, 2% (v/v) 1,4-Dioxane, 4% (w/v) Polyethylene glycol 20000	Resolution 3.30 Å R-free 0.337
6J08 Crystal structure of human MAJIN and TERB2 Deposited 2018-12-21	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 D 174–209（36 aa） Fragment：TERB2 binding motif	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.8；291 K；100 mM HEPES pH 6.8, 0.2 M Potassium thiocyanate, 22% (w/v) Polyethylene glycol 3350, 25% (v/v) Glycerol	Resolution 2.90 Å R-free 0.262
6J08 Crystal structure of human MAJIN and TERB2 Deposited 2018-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 174–209（36 aa） Fragment：TERB2 binding motif	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.8；291 K；100 mM HEPES pH 6.8, 0.2 M Potassium thiocyanate, 22% (w/v) Polyethylene glycol 3350, 25% (v/v) Glycerol	Resolution 2.90 Å R-free 0.262
6J08 Crystal structure of human MAJIN and TERB2 Deposited 2018-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 174–209（36 aa） Fragment：TERB2 binding motif	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.8；291 K；100 mM HEPES pH 6.8, 0.2 M Potassium thiocyanate, 22% (w/v) Polyethylene glycol 3350, 25% (v/v) Glycerol	Resolution 2.90 Å R-free 0.262

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TERB2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–43； UniProt 168–207 Author chain D； PDBConstruct 4–43； UniProt 168–207

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6gny
Deposition date deposition_date	2018-06-01
Structure title title	Crystal structure of the MAJIN-TERB2 heterotetrameric complex
Keywords keywords	Meiosis, telomeres, complex, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	22.53 Å
Radius of gyration Rg (electron density) rg_electron	21.40 Å
Forward intensity I(0) i0	15371200.00
Molecular weight molecular_weight	32047.0 kDa
Excluded volume excluded_volume	41191 Å³
Envelope volume envelope_volume	48965 Å³
Hydration-shell volume shell_volume	19809 Å³
Envelope diameter envelope_diameter	74.1 Å
Shell Rg shell_rg	27.26 Å
Envelope Rg envelope_rg	21.71 Å
Shape Rg shape_rg	21.39 Å
Total Rg total_rg	22.35 Å
Total atoms total_atoms	4543
Residues n_residues	273
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

▼

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

Maximum dimension Dmax dmax	74.4 Å
Rg (real space) rg_real	22.53 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	1.5370e+07
I(0) uncertainty (real space) i0_real_error	1.9880e+05
Rg (reciprocal space) rg_reciprocal	22.53 Å
I(0) (reciprocal space) i0_reciprocal	15370000.0000
Solution quality estimate total_estimate	0.8930
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.7 Å
Skewness Skewness skewness	0.339
Kurtosis Kurtosis kurtosis	-0.428
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4630000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.994

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Membrane-anchored junction protein
Molecular weight formula_weight	12755.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4697

GSMSLKPFTYPFPETRFLHAGPNVYKFKIRYGKSIRGEEIENKEVITQELEDSVRVVLGNLDNLQPFATEHFIVFPYKSKWERVSHLKFKHGEIILIPYPFVFTLYVE

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Telomere repeats-binding bouquet formation protein 2
Molecular weight formula_weight	4750.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSMPVNNMVTGYISIDAMKKFLGELHDFIPGTSGYLAYHVQNE

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	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	119

▶

8. Citations (1)

▶

Unit-cell length a length_a	59.970 Å
Unit-cell length b length_b	88.390 Å
Unit-cell length c length_c	111.670 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	45.350 Å
R factor r_factor	0.1893
R_work r_work	0.1883
R_free r_free	0.2072

fit	/app/data/saxs_computation/gn/6gny/6gny.fit
pddf	/app/data/pr_computation/gn/6gny/6gny.pr.out
profile	/app/data/saxs_computation/gn/6gny/6gny.dat

Crystal structure of the MAJIN-TERB2 heterotetrameric complex

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

Membrane-anchored junction protein

State in the Current Structure

Other States of the Same Protein in the Database

Telomere repeats-binding bouquet formation protein 2

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)