SAXSdb — 4zfo

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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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 1–54	Fragment：Extracellular (N-terminal) domain, UNP residues 1-54	J22.9-xi Fab, Heavy Chain × 1 J22.9-xi Fab, Light Chain × 1 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain K； UniProt 1–54	Fragment：Extracellular (N-terminal) domain, UNP residues 1-54	J22.9-xi Fab, Light Chain × 1 J22.9-xi Fab, Heavy Chain × 1 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

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 4ZFO	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 ligand/ion 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 ligand/ion 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
6J7W Crystal Structure of Human BCMA in complex with UniAb(TM) VH Deposited 2019-01-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 6–44（39 aa）	Not recorded	No recorded non-water small molecule	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
6J7W Crystal Structure of Human BCMA in complex with UniAb(TM) VH Deposited 2019-01-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 6–44（39 aa）	Not recorded	No recorded non-water small molecule	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
8HXQ Nanobody1 in complex with human BCMA ECD Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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 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 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 ligand/ion 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	1
Chains and sequence ranges	Author chain F； PDBConstruct 1–54； UniProt 1–54 Author chain K； PDBConstruct 1–54； UniProt 1–54

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	4zfo
Deposition date deposition_date	2015-04-21
Structure title title	J22.9-xi: chimeric mouse/human antibody against human BCMA (CD269)
Keywords keywords	antibody Fab-ligand complex anti-BCMA anti-tumor, 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	33.83 Å
Radius of gyration Rg (electron density) rg_electron	32.88 Å
Forward intensity I(0) i0	167357000.00
Molecular weight molecular_weight	101230.0 kDa
Excluded volume excluded_volume	125610 Å³
Envelope volume envelope_volume	165040 Å³
Hydration-shell volume shell_volume	41997 Å³
Envelope diameter envelope_diameter	107.9 Å
Shell Rg shell_rg	39.87 Å
Envelope Rg envelope_rg	32.32 Å
Shape Rg shape_rg	32.83 Å
Total Rg total_rg	33.58 Å
Total atoms total_atoms	7103
Residues n_residues	929
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	105.7 Å
Rg (real space) rg_real	33.70 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	1.6740e+08
I(0) uncertainty (real space) i0_real_error	2.8900e+06
Rg (reciprocal space) rg_reciprocal	33.78 Å
I(0) (reciprocal space) i0_reciprocal	167400000.0000
Solution quality estimate total_estimate	0.9094
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	42.7 Å
Skewness Skewness skewness	0.117
Kurtosis Kurtosis kurtosis	-0.613
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14640000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.940

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Tumor necrosis factor receptor superfamily member 17
Molecular weight formula_weight	5903.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,K
Atom count atom_count	7946

MLQMAGQCSQNEYFDSLLHACIPCQLRCSSNTPPLTCQRYCNASVTNSVKGTNA

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	J22.9-xi Fab, Light Chain
Molecular weight formula_weight	23542.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIVMTQSQRFMTTSVGDRVSVTCKASQSVDSNVAWYQQKPRQSPKALIFSASLRFSGVPARFTGSGSGTDFTLTISNLQSEDLAEYFCQQYNNYPLTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEA

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	House Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	J22.9-xi Fab, Heavy Chain
Molecular weight formula_weight	23641.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QVQLQQSGGGLVQPGGSLKLSCAASGIDFSRYWMSWVRRAPGKGLEWIGEINPDSSTINYAPSLKDKFIISRDNAKNTLYLQMSKVRSEDTALYYCASLYYDYGDAMDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPA

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	House Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	J22.9-xi Fab, Light Chain
Molecular weight formula_weight	23471.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DIVMTQSQRFMTTSVGDRVSVTCKASQSVDSNVAWYQQKPRQSPKALIFSASLRFSGVPARFTGSGSGTDFTLTISNLQSEDLAEYFCQQYNNYPLTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	House Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 5 Entity 5 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	209.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	769

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4zfob1
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.1.1.0 — automated matches

Domain ID domain_id	d4zfob2
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.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d4zfof_
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	d4zfok_
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	d4zfol1
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.1.1.0 — automated matches

Domain ID domain_id	d4zfol2
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.1.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	4zfoA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4zfoA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4zfoB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4zfoB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4zfoH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4zfoH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4zfoL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4zfoL02
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	72.801 Å
Unit-cell length b length_b	110.139 Å
Unit-cell length c length_c	137.279 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	1.895 Å
Low-resolution limit resolution_low	42.258 Å
R factor r_factor	0.1779
R_work r_work	0.1762
R_free r_free	0.2090

fit	/app/data/saxs_computation/zf/4zfo/4zfo.fit
pddf	/app/data/pr_computation/zf/4zfo/4zfo.pr.out
profile	/app/data/saxs_computation/zf/4zfo/4zfo.dat

J22.9-xi: chimeric mouse/human antibody against human BCMA (CD269)

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 (7)

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 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)