SAXSdb — 6gnx

▼

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 1–112 Chain C； UniProt 1–112	Non-standard monomer：Yes (specific site not provided by mmCIF)	Telomere repeats-binding bouquet formation protein 2 × 2 （Q8NHR7）	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

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 6GNX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6GNY Crystal structure of the MAJIN-TERB2 heterotetrameric complex 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 1–106（106 aa） Chain C 1–106（106 aa）	Not recorded	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
6J08 Crystal structure of human MAJIN and TERB2 Deposited 2018-12-21	Different construct Different mutation/modification Different oligomeric state 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 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 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 3–114； UniProt 1–112 Author chain C； PDBConstruct 3–114； UniProt 1–112

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 169–220 Chain D； UniProt 169–220	Non-standard monomer：Yes (specific site not provided by mmCIF)	Membrane-anchored junction protein × 2 （Q3KP22）	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

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 6GNX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6GNY Crystal structure of the MAJIN-TERB2 heterotetrameric complex 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 168–207（40 aa） Chain D 168–207（40 aa）	Not recorded	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
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 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 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 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 4–55； UniProt 169–220 Author chain D； PDBConstruct 4–55； UniProt 169–220

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	6gnx
Deposition date deposition_date	2018-06-01
Structure title title	Crystal structure of the MAJIN-TERB2 heterotetrameric complex - selenomethionine derivative
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	22.40 Å
Radius of gyration Rg (electron density) rg_electron	21.32 Å
Forward intensity I(0) i0	14334000.00
Molecular weight molecular_weight	31046.0 kDa
Excluded volume excluded_volume	39824 Å³
Envelope volume envelope_volume	47999 Å³
Hydration-shell volume shell_volume	19442 Å³
Envelope diameter envelope_diameter	72.6 Å
Shell Rg shell_rg	27.34 Å
Envelope Rg envelope_rg	21.74 Å
Shape Rg shape_rg	21.32 Å
Total Rg total_rg	22.23 Å
Total atoms total_atoms	4369
Residues n_residues	258
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	75.8 Å
Rg (real space) rg_real	22.42 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	1.4330e+07
I(0) uncertainty (real space) i0_real_error	1.9840e+05
Rg (reciprocal space) rg_reciprocal	22.42 Å
I(0) (reciprocal space) i0_reciprocal	14330000.0000
Solution quality estimate total_estimate	0.8826
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.0 Å
Skewness Skewness skewness	0.366
Kurtosis Kurtosis kurtosis	-0.406
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3763000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.997

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Membrane-anchored junction protein
Molecular weight formula_weight	13710.5 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	4369

GSMSLKPFTYPFPETRFLHAGPNVYKFKIRYGKSIRGEEIENKEVITQELEDSVRVVLGNLDNLQPFATEHFIVFPYKSKWERVSHLKFKHGEIILIPYPFVFTLYVEMKWFHE

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	6371.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSMVNNMVTGYISIDAMKKFLGELHDFIPGTSGYLAYHVQNEINMSAIKNKLKRK

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

▶

8. Citations (1)

▶

Unit-cell length a length_a	59.880 Å
Unit-cell length b length_b	59.880 Å
Unit-cell length c length_c	159.930 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	49.329 Å
R factor r_factor	0.2589
R_work r_work	0.2542
R_free r_free	0.3039

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

Crystal structure of the MAJIN-TERB2 heterotetrameric complex - selenomethionine derivative

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)