PDB-4x1j: X-ray crystal structure of the dimeric BMP antagonist NBL1

ID or keywords:

Entry

Database: PDB / ID: 4x1j

Title

X-ray crystal structure of the dimeric BMP antagonist NBL1

Components

Neuroblastoma suppressor of tumorigenicity 1

Keywords

BMP Binding Protein / BMP antagonist / DAN family / Cystine-knot

Function / homology

Function and homology information

sequestering of BMP from receptor via BMP binding / sequestering of BMP in extracellular matrix / negative regulation of monocyte chemotaxis / determination of dorsal identity /

morphogen activity / BMP binding / negative regulation of BMP signaling pathway / positive regulation of neuron differentiation / neuron projection morphogenesis / animal organ morphogenesis ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.5 Å

Authors

Thompson, T.B. / Nolan, K. / Kattamuri, C.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2015
Title: Structure of Neuroblastoma Suppressor of Tumorigenicity 1 (NBL1): INSIGHTS FOR THE FUNCTIONAL VARIABILITY ACROSS BONE MORPHOGENETIC PROTEIN (BMP) ANTAGONISTS.
Authors: Nolan, K. / Kattamuri, C. / Luedeke, D.M. / Angerman, E.B. / Rankin, S.A. / Stevens, M.L. / Zorn, A.M. / Thompson, T.B.

History

Deposition	Nov 24, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Feb 18, 2015	Group: Database references
Revision 1.2	Mar 4, 2015	Group: Database references
Revision 1.3	Aug 17, 2016	Group: Structure summary
Revision 1.4	Sep 20, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4x1j.cif.gz	84.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4x1j.ent.gz	67.4 KB	Display	PDB format
PDBx/mmJSON format	4x1j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x1/4x1j ftp://data.pdbj.org/pub/pdb/validation_reports/x1/4x1j	HTTPS FTP

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Related structure data

Related structure data	4jph
Similar structure data	5ufk-d 4hbq-2 5f44-2 5hdl-1 4nx9-d 5hdl-2 1c3g-d 5hbb-1 5j4m-2 4jph-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (1) #68 - Aug 2005 Neurotrophins similarity (1)

Deposited unit

A: Neuroblastoma suppressor of tumorigenicity 1

B: Neuroblastoma suppressor of tumorigenicity 1

hetero molecules

25.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	59.665, 59.665, 145.018
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	0	1	0	A	29 - 124
2	0	1	0	B	29 - 124

#1: Protein

Neuroblastoma suppressor of tumorigenicity 1 / DAN domain family member 1 / Protein N03 / Zinc finger protein DAN

Mass: 12653.468 Da / Num. of mol.: 2 / Fragment: UNP residues 52-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: NBL1, DAN, DAND1 / Production host:

Escherichia coli (E. coli) / References: UniProt: P41271

#2: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#3: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.55 Å³/Da / Density % sol: 56.41 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.1 MES/imidazole (pH 6.5) and 0.02M of several amino acids (sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine)

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 7, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.5→55.18 Å / Num. obs: 9690 / % possible obs: 99.68 % / Redundancy: 12.3 % / Net I/σ(I): 23.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Resolution: 2.5→55.18 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.914 / SU B: 21.712 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27315	964	10 %	RANDOM
R_work	0.21576	-	-	-
obs	0.22175	8674	99.68 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 89.054 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.25 Å²	0 Å²	0 Å²
2-	-	0.25 Å²	0 Å²
3-	-	-	-0.49 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→55.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1330	0	28	5	1363

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	1394
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	1279
X-RAY DIFFRACTION	r_angle_refined_deg	1.523	1.956	1886
X-RAY DIFFRACTION	r_angle_other_deg	1.011	3	2965
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.8	5	172
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.874	25.66	53
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.946	15	236
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.462	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	212
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	1526
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	285
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	6.921	3.507	703
X-RAY DIFFRACTION	r_mcbond_other	6.921	3.504	702
X-RAY DIFFRACTION	r_mcangle_it	9.017	5.173	870
X-RAY DIFFRACTION	r_mcangle_other	9.013	5.176	871
X-RAY DIFFRACTION	r_scbond_it	12.385	4.769	691
X-RAY DIFFRACTION	r_scbond_other	12.152	4.776	691
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	15.747	6.887	1017
X-RAY DIFFRACTION	r_long_range_B_refined	16.68	29.775	1419
X-RAY DIFFRACTION	r_long_range_B_other	16.676	29.915	1420
X-RAY DIFFRACTION	r_rigid_bond_restr	3.331	3	2673
X-RAY DIFFRACTION	r_sphericity_free		5	3
X-RAY DIFFRACTION	r_sphericity_bonded	43.6	5	2639

Refine LS restraints NCS

Ens-ID: 1 / Number: 3491 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 2.5→2.564 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.35	67	-
R_work	0.302	600	-
obs	-	-	96.81 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	13.1876	1.714	0.6252	10.6773	0.7218	18.465	0.3029	1.3818	0.927	-1.4753	0.4306	-1.172	0.0685	1.9211	-0.7335	0.6667	0.1816	-0.035	0.4448	-0.0484	0.5045	76.561	137.113	18.182
2	9.0639	-4.415	-5.9099	19.8592	10.8323	23.7725	0.5386	-0.9159	1.0829	0.455	-0.223	-0.0357	-0.2189	0.6499	-0.3156	0.4516	-0.0814	0.085	0.3368	-0.0614	0.2827	62.072	142.375	35.474
3	27.5656	-0.6116	10.8769	25.7287	7.0132	8.806	-2.2951	1.2947	2.9161	-1.1704	-1.439	3.4459	-1.3564	-0.5426	3.7341	0.7572	0.0751	-0.2458	1.2467	-0.7695	2.0317	46.635	149.922	42.59
4	3.6294	-0.2525	-5.2465	3.5001	1.5132	13.4457	-0.251	-0.3614	-0.0094	0.6064	-0.0842	0.4194	0.8459	0.1575	0.3353	0.2326	-0.0226	0.0219	0.1414	0.0212	0.2143	64.345	139.028	22.526
5	3.1005	-0.8477	-3.3781	5.5368	0.1752	22.199	-0.3887	0.2559	-0.0931	-0.2894	-0.0692	0.7613	1.5856	-1.0896	0.4578	0.2998	-0.1466	-0.0045	0.2187	-0.0914	0.5011	60.114	134.094	15.057
6	3.7934	-1.2428	-0.7603	3.6412	-3.7543	12.9331	-0.444	0.4008	0.3099	0.4966	0.9278	0.6832	-0.2458	-2.3113	-0.4838	0.985	-0.1603	0.6913	0.9794	0.0535	0.944	44.846	141.709	42.985
7	2.7839	2.8724	-5.3521	9.727	-0.1884	14.7012	0.1048	0.1143	0.3847	1.0975	-0.3638	1.61	0.848	-0.8494	0.2591	0.6473	-0.2601	0.292	0.4378	-0.0594	0.5061	58.437	133.821	26.031
8	15.9665	2.6758	5.4671	18.6738	9.755	17.469	0.4145	-1.488	-0.0185	1.5329	0.0718	-0.8164	0.5628	1.6181	-0.4862	0.2643	-0.0233	0.0136	0.9747	0.02	0.193	74.449	144.761	15.506
9	0.956	-0.3426	0.4802	1.6848	2.8331	10.391	0.1169	0.2173	-0.0787	-0.1377	0.0774	-0.0262	-0.1622	0.3127	-0.1943	0.2636	0.0201	-0.0278	0.1809	0.0068	0.2008	68.554	138.589	0.819
10	60.199	-47.9338	-19.7014	104.6813	-7.6775	14.6649	3.3843	-0.289	-1.0114	8.3307	-2.4096	3.7221	-5.0455	1.0951	-0.9747	5.1709	1.732	1.8356	4.372	0.6595	0.8163	51.119	144.006	27.311
11	1.1745	0.0359	4.1648	1.4475	1.09	17.9183	-0.0492	0.1789	0.0571	-0.3606	-0.1236	0.2578	-0.8683	0.0756	0.1728	0.3285	0.0861	-0.0111	0.2842	-0.0178	0.2163	62.748	145.847	3.644
12	8.9548	-1.0098	3.1957	11.145	10.2474	24.0364	0.4019	1.0275	-0.4936	-0.4494	-0.4348	0.392	0.7545	-0.365	0.0329	0.2972	0.078	-0.0588	0.278	-0.0015	0.2088	62.944	135.7	-21.183
13	2.3656	-1.0993	-1.435	4.0314	0.9828	13.5121	0.1459	0.3107	-0.0918	-0.2653	-0.2309	0.1076	-0.7729	-0.1883	0.085	0.3539	0.0216	-0.0578	0.2507	-0.0271	0.1549	65.705	146.845	4.33
14	16.3951	1.9605	11.0561	2.0677	-6.2404	41.0776	0.5383	0.3477	-0.5646	-0.0695	0.1809	-0.1992	0.5215	0.3276	-0.7191	0.6599	0.2788	0.0588	0.5271	-0.2188	0.45	58.089	145.946	3.211

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	30 - 34
2	X-RAY DIFFRACTION	2	A	35 - 42
3	X-RAY DIFFRACTION	3	A	43 - 51
4	X-RAY DIFFRACTION	4	A	52 - 68
5	X-RAY DIFFRACTION	5	A	69 - 90
6	X-RAY DIFFRACTION	6	A	91 - 111
7	X-RAY DIFFRACTION	7	A	112 - 124
8	X-RAY DIFFRACTION	8	B	30 - 35
9	X-RAY DIFFRACTION	9	B	36 - 69
10	X-RAY DIFFRACTION	10	B	77 - 79
11	X-RAY DIFFRACTION	11	B	80 - 92
12	X-RAY DIFFRACTION	12	B	93 - 112
13	X-RAY DIFFRACTION	13	B	113 - 122
14	X-RAY DIFFRACTION	14	B	123 - 129

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