PDB-9d77: Crystal form of Netrin-1 mimics nanotubes

ID or keywords:

Entry

Database: PDB / ID: 9d77

Title

Crystal form of Netrin-1 mimics nanotubes

Components

Netrin-1

Keywords

SIGNALING PROTEIN / APOPTOSIS / Axon guidance cue / nanotubes

Function / homology

Function and homology information

regulation of glial cell migration / chemorepulsion of axon / anterior/posterior axon guidance / Cdc42 protein signal transduction / motor neuron migration / tissue development / negative regulation of axon extension / substrate-dependent cell migration, cell extension / motor neuron axon guidance / nuclear migration ...
Similarity search - Function

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 3.4 Å

Authors

Meier, M. / Krahn, N.J. / McDougall, M.D. / Rafiei, F. / Koch, M. / Stetefeld, J.

Funding support

Canada,

Germany, 2items

Citation

Journal: To Be Published
Title: Mechanistic insights in the higher-order protein assemblies of netrin-1
Authors: Rafiei, F. / Meier, M. / Koch, M. / Stetefeld, J.

History

Deposition	Aug 16, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9d77.cif.gz	256 KB	Display	PDBx/mmCIF format
PDB format	pdb9d77.ent.gz		Display	PDB format
PDBx/mmJSON format	9d77.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9d77_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	9d77_full_validation.pdf.gz	1.3 MB	Display
Data in XML	9d77_validation.xml.gz	20.4 KB	Display
Data in CIF	9d77_validation.cif.gz	26.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d7/9d77 ftp://data.pdbj.org/pub/pdb/validation_reports/d7/9d77	HTTPS FTP

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Related structure data

Related structure data	7ler
Similar structure data	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

Deposited unit

A: Netrin-1

hetero molecules

53 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Netrin-1

hetero molecules

A: Netrin-1

hetero molecules

defined by author&software
Evidence: SAXS, Experimental evidence for monomer-dimer equilibrium by SEC-SAXS, SEC-MALS and sedimentation velocity experiments.
106 kDa, 2 polymers

Unit cell

Length a, b, c (Å)	189.260, 189.260, 45.880
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	168
Space group name H-M	P6

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Protein , 1 types, 1 molecules A

#1: Protein	Netrin-1 Mass: 49579.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: NTN1 / Cell (production host): Embryonic kidney cell / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / Tissue (production host): Embryonic kidney / References: UniProt: Q90922

#1: Protein

Netrin-1

Mass: 49579.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Gallus gallus (chicken) / Gene: NTN1 / Cell (production host): Embryonic kidney cell / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host:

Homo sapiens (human) / Tissue (production host): Embryonic kidney / References: UniProt: Q90922

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Sugars , 3 types, 4 molecules

#2: Polysaccharide

alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...

Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}	LINUCS	PDB-CARE

#3: Polysaccharide

alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...

Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}	LINUCS	PDB-CARE

#4: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated 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

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Non-polymers , 4 types, 24 molecules

#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.53 Å³/Da / Density % sol: 72.86 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 40% v/v 2-methyl-2,4-pentanediol; 5% w/v polyethylene glycol 8000; 100 mM 2-(N-morpholino)ethanesulfonic acid; pH 6.5 Temp details: Crystallisation cabinet

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Data collection

Diffraction

Mean temperature: 100 K / Ambient temp details: X-stream 2000 / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å

Detector

Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 26, 2017 / Details: Rigaku Osmic Confocal Max-Flux multilayer mirror

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.54187 Å / Relative weight: 1

Reflection

Resolution: 3.4→35.77 Å / Num. obs: 9185 / % possible obs: 68.9 % / Redundancy: 9.6 % / B_iso Wilson estimate: 83.7 Å² / CC_1/2: 0.994 / CC star: 0.999 / R_merge(I) obs: 0.412 / R_pim(I) all: 0.14 / R_rim(I) all: 0.435 / Net I/av σ(I): 5.6 / Net I/σ(I): 4.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	% possible all
4.2-35.77	9.6	0.338	5.8	7111	0.995	0.999	0.116	0.357	99.51
4.2-4.5	9.8	1.166	2.4	1312	0.67	0.896	0.393	1.232	100
3.4-4.2	9.8	1.473	1.9	2074	0.583	0.729	0.488	1.553	33.53

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
HKL-3000		data collection
XDS	Jun 30, 2023 BUILT=20230630	data reduction
XSCALE	Jun 30, 2023 BUILT=20230630	data scaling
PHASER	2.8.3	phasing
Coot	0.9.8.95	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.4→35.77 Å / Cor.coef. F_o:F_c: 0.857 / Cor.coef. F_o:F_c free: 0.805 / SU B: 170.905 / SU ML: 1.034 / Cross valid method: THROUGHOUT / ESU R Free: 0.864
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3348	743	8.089 %	Random selection
R_work	0.2967	8442	-	-
all	0.3	-	-	-
obs	-	9185	68.74 %	-

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 0.85 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 88.104 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.198 Å²	-2.099 Å²	-0 Å²
2-	-	-4.198 Å²	0 Å²
3-	-	-	13.618 Å²

Refinement step

Cycle: LAST / Resolution: 3.4→35.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3272	0	225	20	3517

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	3679
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3254
X-RAY DIFFRACTION	r_angle_refined_deg	1.847	1.895	5023
X-RAY DIFFRACTION	r_angle_other_deg	0.6	1.845	7565
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	10.352	4.693	483
X-RAY DIFFRACTION	r_dihedral_angle_other_1_deg	8.932	10	8
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.406	5	35
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.949	9.98	601
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	0.478	4	1
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.042	10	170
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	570
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	4266
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	863
X-RAY DIFFRACTION	r_nbd_refined	0.181	0.2	674
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.195	0.2	3184
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	1739
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.107	0.2	1950
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.281	0.2	114
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.162	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.105	0.2	28
X-RAY DIFFRACTION	r_nbd_other	0.162	0.2	107
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.182	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	0.338	0.469	1697
X-RAY DIFFRACTION	r_mcbond_other	0.338	0.469	1697
X-RAY DIFFRACTION	r_mcangle_it	0.61	0.839	2124
X-RAY DIFFRACTION	r_mcangle_other	0.61	0.839	2125
X-RAY DIFFRACTION	r_scbond_it	0.864	0.958	1982
X-RAY DIFFRACTION	r_scbond_other	0.864	0.957	1983
X-RAY DIFFRACTION	r_scangle_it	1.532	1.779	2902
X-RAY DIFFRACTION	r_scangle_other	1.532	1.779	2903
X-RAY DIFFRACTION	r_lrange_it	2.853	7.414	14412
X-RAY DIFFRACTION	r_lrange_other	2.853	7.414	14412

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.4-3.582	0.35	12	0.412	281	X-RAY DIFFRACTION	15.3403
3.582-3.797	0.371	50	0.347	454	X-RAY DIFFRACTION	27.8607
3.797-4.056	0.378	55	0.337	692	X-RAY DIFFRACTION	43.761
4.056-4.376	0.375	119	0.365	1209	X-RAY DIFFRACTION	84.6939
4.376-4.787	0.339	118	0.339	1336	X-RAY DIFFRACTION	99.1814
4.787-5.34	0.36	97	0.308	1236	X-RAY DIFFRACTION	99.4034
5.34-6.143	0.442	98	0.31	1091	X-RAY DIFFRACTION	99.5812
6.143-7.469	0.265	82	0.26	942	X-RAY DIFFRACTION	99.8051
7.469-10.34	0.278	63	0.212	744	X-RAY DIFFRACTION	99.6296
10.34-35.77	0.268	49	0.209	457	X-RAY DIFFRACTION	98.6355

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	3.4749	2.6883	2.4287	5.2002	2.9721	3.8675	0.3762	-0.5052	0.6125	0.5017	-0.5876	0.4647	0.0391	-1.0033	0.2113	1.0661	-0.3091	0.0436	1.3777	0.0033	0.1364	43.11	-50.852	-26.957
2	4.8058	2.0352	-0.7998	2.2151	0.7945	1.0897	0.3981	-0.2326	0.7429	0.17	-0.8326	0.9449	-0.1637	-0.6092	0.4345	1.81	-0.1953	-0.1658	1.2805	-0.258	0.4516	57.197	-26.111	-16.432
3	8.5333	-1.0215	0.7064	0.1246	-0.1123	1.6201	0.0205	0.7761	-0.3155	-0.0492	-0.0941	0.0415	0.03	-0.1787	0.0736	1.3255	-0.0713	-0.1243	0.6116	-0.0991	0.0373	76.503	-10.088	-10.754
4	7.9865	0.0523	-1.4983	0.0286	-0.2681	3.03	0.1051	-0.4239	0.9289	-0.0349	0.0373	0.0026	-0.3701	-0.2348	-0.1424	1.2758	0.0503	0.0186	0.7128	-0.0487	0.1085	96.864	14.224	-5.994
5	1.644	0.7734	-6.6744	1.0539	-4.707	30.8333	0.5743	-0.1831	0.1292	-0.2544	-0.0812	-0.0065	-0.918	1.1163	-0.4931	1.3204	0.0246	-0.661	1.3123	0.0744	1.0219	21.164	-44.552	-56.182
6	2.37	-1.4179	1.8785	11.1903	-14.3459	18.3979	-0.7904	-0.6456	-0.4724	-0.4649	-0.2996	-0.8297	0.5333	0.3442	1.0899	1.1061	-0.0243	0.1207	0.8359	-0.2112	0.6832	57.75	-53.157	-42.518
7	7.77	-5.9445	-9.8986	4.5616	7.5782	12.6125	-0.5829	0.5578	-0.695	0.4575	-0.2999	0.5483	0.7467	-0.665	0.8828	0.8204	-0.2545	-0.2893	1.3592	0.3284	0.6142	94.382	-6.033	4.948
8	773.9279	-373.2213	-112.5057	180.1714	54.1285	16.4404	2.3183	4.9366	4.9768	-1.024	-1.8452	-2.7304	-0.3719	-1.0669	-0.4731	1.2936	-0.1133	0.1857	1.5418	-0.9452	0.7097	80.55	-31.034	-13.896
9	11.2986	6.8435	-31.1871	4.1512	-18.8949	86.0898	1.6916	0.0113	0.584	1.0429	-0.071	0.3591	-4.7273	0.0248	-1.6206	1.0317	-0.1122	0.0728	0.8888	-0.0821	0.0663	103.106	7.58	-4.104

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	37 - 286
2	X-RAY DIFFRACTION	1	ALL	A	458
3	X-RAY DIFFRACTION	1	ALL	W	1 - 20
4	X-RAY DIFFRACTION	1	ALL	A	37 - 286
5	X-RAY DIFFRACTION	1	ALL	A	458
6	X-RAY DIFFRACTION	1	ALL	W	1 - 20
7	X-RAY DIFFRACTION	2	ALL	A	287 - 341
8	X-RAY DIFFRACTION	2	ALL	W	21 - 22
9	X-RAY DIFFRACTION	2	ALL	A	287 - 341
10	X-RAY DIFFRACTION	2	ALL	W	21 - 22
11	X-RAY DIFFRACTION	3	ALL	A	342 - 404
12	X-RAY DIFFRACTION	3	ALL	C	1
13	X-RAY DIFFRACTION	3	ALL	W	23
14	X-RAY DIFFRACTION	3	ALL	A	342 - 404
15	X-RAY DIFFRACTION	3	ALL	C	1
16	X-RAY DIFFRACTION	3	ALL	W	23
17	X-RAY DIFFRACTION	4	ALL	A	405 - 456
18	X-RAY DIFFRACTION	4	ALL	W	24 - 25
19	X-RAY DIFFRACTION	4	ALL	A	405 - 456
20	X-RAY DIFFRACTION	4	ALL	W	24 - 25
21	X-RAY DIFFRACTION	5	ALL	A	470 - 474
22	X-RAY DIFFRACTION	5	ALL	A	470 - 474
23	X-RAY DIFFRACTION	6	ALL	A	459 - 464
24	X-RAY DIFFRACTION	6	ALL	A	459 - 464
25	X-RAY DIFFRACTION	7	ALL	A	465 - 469
26	X-RAY DIFFRACTION	7	ALL	A	465 - 469
27	X-RAY DIFFRACTION	8	ALL	L	2
28	X-RAY DIFFRACTION	8	ALL	L	2
29	X-RAY DIFFRACTION	9	ALL	L	3
30	X-RAY DIFFRACTION	9	ALL	L	3

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