SAXSdb — 6j7w

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

Tumor necrosis factor receptor superfamily member 17

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 6–44	Not recorded	UniAb × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；0.2M sodium malonate pH 4.0 and 20% PEG 3350	Resolution 2.60 Å R-free 0.271
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 6–44	Not recorded	UniAb × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；0.2M sodium malonate pH 4.0 and 20% PEG 3350	Resolution 2.60 Å R-free 0.271

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 6J7W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OQD Crystal structure of sTALL-1 and BCMA Deposited 2003-03-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 108 PDB declaration: 108-meric	Chain K 8–46（39 aa） Fragment：extracellular domain Chain L 8–46（39 aa） Fragment：extracellular domain Chain M 8–46（39 aa） Fragment：extracellular domain Chain N 8–46（39 aa） Fragment：extracellular domain Chain O 8–46（39 aa） Fragment：extracellular domain Chain P 8–46（39 aa） Fragment：extracellular domain Chain Q 8–46（39 aa） Fragment：extracellular domain Chain R 8–46（39 aa） Fragment：extracellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；277 K；dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.260
1XU2 The crystal structure of APRIL bound to BCMA Deposited 2004-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 5–51（47 aa） Fragment：BCMA ECD Chain S 5–51（47 aa） Fragment：BCMA ECD Chain T 5–51（47 aa） Fragment：BCMA ECD	Not recorded	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；292 K；well solution: 0.1M MES, 5% Peg 8000, 10% Peg 1000, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.35 Å R-free 0.213
2KN1 Solution NMR Structure of BCMA Deposited 2009-08-11	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 2–50（49 aa） Fragment：residues 2-50	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；Ionic strength (raw mmCIF value) 10；Pressure ambient NMR sample composition 900 uM BCMA, 10 mM sodium phosphate, 0.02 % sodium azide, 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
4ZFO J22.9-xi: chimeric mouse/human antibody against human BCMA (CD269) Deposited 2015-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–54（54 aa） Fragment：Extracellular (N-terminal) domain, UNP residues 1-54	Not recorded	CU COPPER (II) ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；1 microliter of the complex at 8 mg/ml with 2 microliters of 21% PEG 3350, 0.1 M BisTris pH 6.5 and 5 mM CuCl2	Resolution 1.90 Å R-free 0.209
4ZFO J22.9-xi: chimeric mouse/human antibody against human BCMA (CD269) Deposited 2015-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 1–54（54 aa） Fragment：Extracellular (N-terminal) domain, UNP residues 1-54	Not recorded	CU COPPER (II) ION × 2 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；1 microliter of the complex at 8 mg/ml with 2 microliters of 21% PEG 3350, 0.1 M BisTris pH 6.5 and 5 mM CuCl2	Resolution 1.90 Å R-free 0.209
8HXQ Nanobody1 in complex with human BCMA ECD Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–54（54 aa） Chain D 1–54（54 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；293 K；0.2 M Ammonium sulfate, 20% w/v Polyethylene glycol 3350, pH6.1	Resolution 2.40 Å R-free 0.274
8HXR Nanobody2 in complex with human BCMA ECD Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–54（54 aa） Chain D 1–54（54 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.8 M Sodium acetate trihydrate, 0.1 M Bis-Tris Propane pH7.0	Resolution 2.70 Å R-free 0.287
8QY9 J22.9-H, fully humanized Fab Fragment based on chimeric J22.9-xi IgG against BCMA Deposited 2023-10-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 7–41（35 aa）	Not recorded	CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；14% PEG 3350 100 mM BisTris 7.5 mM Cu(II)	Resolution 3.10 Å R-free 0.301
8QYA J22.9-FNY, fully humanized, CDR optimized Fab Fragment based on chimeric J22.9-xi IgG against BCMA; with VH CDR2 glycosylation Deposited 2023-10-25	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 6–41（36 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 3350 CuCl2 BisTris	Resolution 2.72 Å R-free 0.299
8QYB J22.9-ISY, fully humanized and CDR optimized Fab Fragment based on chimeric J22.9-xi IgG against BCMA Deposited 2023-10-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 7–41（35 aa）	Not recorded	CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；14% PEG 3350 7.5 mM CuCl2 BisTris	Resolution 3.09 Å R-free 0.288
9MQO Crystal structure of BCMA in complex with CA10v2 Fab Deposited 2025-01-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric	Chain A 1–54（54 aa） Chain D 1–54（54 aa） Chain G 1–54（54 aa） Chain J 1–54（54 aa） Chain M 1–54（54 aa） Chain P 1–54（54 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.18 M Sodium Chloride, 0.09 M Phosphate/citrate pH 4.2, 20 % w/v PEG 8000, 0.1M Sodium Malonate	Resolution 3.18 Å R-free 0.272

10 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TNR17_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–39； UniProt 6–44 Author chain D； PDBConstruct 1–39； UniProt 6–44

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	6j7w
Deposition date deposition_date	2019-01-18
Structure title title	Crystal Structure of Human BCMA in complex with UniAb(TM) VH
Keywords keywords	Heavy chain antibodies, VH domains, domain antibodies, IMMUNE SYSTEM; 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	22.41 Å
Radius of gyration Rg (electron density) rg_electron	21.76 Å
Forward intensity I(0) i0	21746300.00
Molecular weight molecular_weight	33023.0 kDa
Excluded volume excluded_volume	40259 Å³
Envelope volume envelope_volume	49773 Å³
Hydration-shell volume shell_volume	19636 Å³
Envelope diameter envelope_diameter	78.4 Å
Shell Rg shell_rg	27.63 Å
Envelope Rg envelope_rg	21.95 Å
Shape Rg shape_rg	21.74 Å
Total Rg total_rg	22.57 Å
Total atoms total_atoms	2311
Residues n_residues	311
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	76.8 Å
Rg (real space) rg_real	22.44 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	2.1750e+07
I(0) uncertainty (real space) i0_real_error	2.9480e+05
Rg (reciprocal space) rg_reciprocal	22.43 Å
I(0) (reciprocal space) i0_reciprocal	21750000.0000
Solution quality estimate total_estimate	0.8793
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.4 Å
Skewness Skewness skewness	0.380
Kurtosis Kurtosis kurtosis	-0.343
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4710000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.985

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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	UniAb
Molecular weight formula_weight	12588.8 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	2345

EVQLVESGGGLVQPGGSLRLSCAASGFTVSSYGMSWVRQAPGKGPEWVSGIRGSDGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKQGENDGPFDHRGQGTLVTVS

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Tumor necrosis factor receptor superfamily member 17
Molecular weight formula_weight	4355.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GQCSQNEYFDSLLHACIPCQLRCSSNTPPLTCQRYCNAS

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	Homo sapiens

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6j7wa_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6j7wb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6j7wc_
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.2 — BAFF receptor-like

Domain ID domain_id	d6j7wd_
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.2 — BAFF receptor-like

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8. Citations (1)

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Unit-cell length a length_a	65.392 Å
Unit-cell length b length_b	73.806 Å
Unit-cell length c length_c	133.491 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	2.600 Å
Low-resolution limit resolution_low	48.990 Å
R factor r_factor	0.2118
R_work r_work	0.2085
R_free r_free	0.2713

fit	/app/data/saxs_computation/j7/6j7w/6j7w.fit
pddf	/app/data/pr_computation/j7/6j7w/6j7w.pr.out
profile	/app/data/saxs_computation/j7/6j7w/6j7w.dat

Crystal Structure of Human BCMA in complex with UniAb(TM) VH

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

Tumor necrosis factor receptor superfamily member 17

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

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)