PDB-4edx: Nerve Growth Factor in Complex with Fab from mouse mAb 911

ID or keywords:

Entry

Database: PDB / ID: 4edx

Title

Nerve Growth Factor in Complex with Fab from mouse mAb 911

Components

Beta-nerve growth factor
heavy chain of Fab of murine anti-NGF
light chain of FAB of murine anti-NGF

Keywords

IMMUNE SYSTEM / cystine knot / immunoglobulin / growth/survival factor

Function / homology

Function and homology information

NFG and proNGF binds to p75NTR / Ceramide signalling / nerve growth factor receptor binding / NGF processing / TRKA activation by NGF / PLC-gamma1 signalling / Signalling to STAT3 / p75NTR negatively regulates cell cycle via SC1 / metalloendopeptidase inhibitor activity / nerve growth factor signaling pathway ...
Similarity search - Function

Biological species

Homo sapiens (human)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Eigenbrot, C. / Ultsch, M.

Citation

Journal: MAbs
Title: Generation of a high-fidelity antibody against nerve growth factor using library scanning mutagenesis and validation with structures of the initial and optimized Fab-antigen complexes.
Authors: La Porte, S.L. / Eigenbrot, C. / Ultsch, M. / Ho, W.H. / Foletti, D. / Forgie, A. / Lindquist, K.C. / Shelton, D.L. / Pons, J.

History

Deposition	Mar 27, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 2, 2014	Provider: repository / Type: Initial release
Revision 1.1	Aug 13, 2014	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4edx.cif.gz	415.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4edx.ent.gz	353.8 KB	Display	PDB format
PDBx/mmJSON format	4edx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4edx_validation.pdf.gz	465.8 KB	Display	wwPDB validaton report
Full document	4edx_full_validation.pdf.gz	478.1 KB	Display
Data in XML	4edx_validation.xml.gz	37.4 KB	Display
Data in CIF	4edx_validation.cif.gz	52.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ed/4edx ftp://data.pdbj.org/pub/pdb/validation_reports/ed/4edx	HTTPS FTP

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Related structure data

Related structure data	4edwC C: citing same article (ref.)
Similar structure data	2vxs-1 2vxs-2 7czf-1 7cze-1 7cze-2 4jkx-1 7cze-3 4qhu-d 2fss-3 4gf1-d 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	#68 - Aug 2005 Neurotrophins similarity (30) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (4) #88 - Apr 2007 Clathrin similarity (1) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (1) #60 - Dec 2004 Ubiquitin similarity (3) #148 - Apr 2012 Ras Protein similarity (2) #56 - Aug 2004 Caspases similarity (1) #245 - May 2020 Spliceosomes similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (3) #28 - Apr 2002 Anthrax Toxin similarity (1) #122 - Feb 2010 Enhanceosome similarity (1)

PDB pages

PDBj /

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NCBI

Related items in Molecule of the Month

#68 - Aug 2005
Neurotrophins
similarity (30)
#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#195 - Mar 2016
RAF Protein Kinases
similarity (4)
#88 - Apr 2007
Clathrin
similarity (1)
#267 - Mar 2022
Vascular Endothelial Growth Factor (VegF
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (3)
#148 - Apr 2012
Ras Protein
similarity (2)
#56 - Aug 2004
Caspases
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (3)
#28 - Apr 2002
Anthrax Toxin
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)

Deposited unit

W: Beta-nerve growth factor

A: light chain of FAB of murine anti-NGF

B: heavy chain of Fab of murine anti-NGF

V: Beta-nerve growth factor

L: light chain of FAB of murine anti-NGF

H: heavy chain of Fab of murine anti-NGF

122 kDa, 6 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)	57.748, 69.931, 83.736
Angle α, β, γ (deg.)	104.34, 94.13, 110.42
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	V
2	1	W
1	2	L
2	2	A
1	3	H
2	3	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	3	V	10 - 60
2	1	1	3	W	10 - 60
1	2	1	3	V	67 - 115
2	2	1	3	W	67 - 115
1	1	2	3	L	1 - 214
2	1	2	3	A	1 - 214
1	1	3	3	H	2 - 99
2	1	3	3	B	2 - 99
1	2	3	3	H	101 - 190
2	2	3	3	B	101 - 190
1	3	3	6	H	191 - 200
2	3	3	6	B	191 - 200
1	4	3	3	H	201 - 228
2	4	3	3	B	201 - 228

NCS ensembles :

ID
1
2
3

#1: Protein	Beta-nerve growth factor / Beta-NGF Mass: 13515.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NGF, NGFB / Production host: Escherichia coli (E. coli) / References: UniProt: P01138
#2: Antibody	light chain of FAB of murine anti-NGF Mass: 23779.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Antibody	heavy chain of Fab of murine anti-NGF Mass: 23681.402 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.38 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: PEG 3350, zinc acetate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 6, 2006
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. all: 38098 / Num. obs: 38098 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 2.5 % / B_iso Wilson estimate: 57 Å² / R_sym value: 0.067 / Net I/σ(I): 13

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
REFMAC	5.1.24	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→30.49 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.899 / SU B: 10.386 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.698 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2579	1015	2.6 %	RANDOM
R_work	0.20804	-	-	-
all	0.20932	37866	-	-
obs	0.20932	37866	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 52.337 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.14 Å²	0.45 Å²	1.74 Å²
2-	-	-0.19 Å²	-0.07 Å²
3-	-	-	-1.42 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→30.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8200	0	0	98	8298

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.021	8398
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	7233
X-RAY DIFFRACTION	r_angle_refined_deg	1.116	1.938	11420
X-RAY DIFFRACTION	r_angle_other_deg	0.768	3	16951
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.165	5	1054
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	1289
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	9292
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1688
X-RAY DIFFRACTION	r_nbd_refined	0.169	0.2	1300
X-RAY DIFFRACTION	r_nbd_other	0.217	0.2	8236
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.082	0.2	5384
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	155
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	0.104	0.2	8
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.22	0.2	37
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.214	0.2	10
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	2.196	2.5	5272
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.669	5	8560
X-RAY DIFFRACTION	r_scbond_it	2.323	2.5	3125
X-RAY DIFFRACTION	r_scangle_it	3.547	5	2857
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	V	591	tight positional	0.02	0.05
2	L	1262	tight positional	0.02	0.05
3	H	1169	tight positional	0.03	0.05
1	V	905	loose positional	0.44	5
2	L	1852	loose positional	0.39	5
3	H	1812	loose positional	0.31	5
1	V	591	tight thermal	0.05	0.5
2	L	1262	tight thermal	0.06	0.5
3	H	1169	tight thermal	0.06	0.5
1	V	905	loose thermal	1.19	10
2	L	1852	loose thermal	1.34	10
3	H	1812	loose thermal	1.28	10

LS refinement shell

Resolution: 2.5→2.551 Å / Total num. of bins used: 25 /

	R_factor	Num. reflection
R_free	0.352	61
R_work	0.309	2236

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	3.0872	0.4081	1.7451	1.5116	1.2691	3.0475	-0.1702	0.1059	0.2303	0.0046	0.0392	0.1079	-0.2533	0.3285	0.131	0.1157	-0.0237	-0.0005	0.1672	0.065	0.1635	17.884	4.031	13.639
2	4.2231	-0.3618	-3.3964	0.4242	1.2821	5.6786	-0.2122	-0.4744	0.2213	0.2778	0.1838	-0.1057	0.0661	0.4527	0.0285	0.3531	0.0481	-0.0376	0.1187	-0.056	0.1156	11.531	14.967	49.282
3	2.5093	0.7303	-1.5118	0.7719	-0.5287	3.1275	0.1141	0.0928	0.0768	0.014	-0.0665	-0.0353	-0.1302	-0.0662	-0.0476	0.0962	0.0503	0.0374	0.0836	0.0556	0.1141	-3.667	8.117	11.714
4	4.9624	0.253	0.3596	1.9728	1.029	2.5405	-0.0417	-0.0708	0.6447	0.3657	-0.0921	0.084	-0.2911	-0.1907	0.1338	0.3218	0.0367	-0.0203	0.0051	-0.0004	0.2068	2.579	23.72	39.155
5	4.9581	0.3353	-2.3528	1.3266	-0.0845	2.0164	0.0374	-0.2673	-0.156	-0.0184	-0.0871	0.0253	-0.1285	0.1381	0.0497	0.0933	0.0055	-0.0241	0.1587	0.0525	0.1069	23.139	16.667	-38.995
6	1.2577	1.0477	0.9007	1.4631	1.1572	3.0968	0.077	0.1028	-0.1455	-0.175	-0.0798	-0.1342	0.282	0.1636	0.0028	0.1169	0.1127	0.0225	0.1457	0.0087	0.0477	36.9	8.784	-73.359
7	1.3872	0.5104	-0.141	1.3653	0.5136	5.7692	-0.0155	0.2136	-0.1153	-0.0353	0.0354	0.1729	0.3833	-0.2885	-0.0199	0.1461	-0.0254	-0.0306	0.1536	-0.0328	0.1659	9.803	-0.056	-43.74
8	5.2045	0.4084	0.4428	2.8957	-0.0441	2.4372	0.1915	0.218	-0.5243	0.0228	-0.2368	-0.2729	0.5057	0.1034	0.0452	0.2877	0.0975	-0.0702	0.0439	0.0192	0.187	32.914	-4.961	-65.867
9	1.5459	0.8166	-0.9182	1.5819	0.5046	2.6785	-0.1129	0.0283	-0.1382	-0.0724	-0.0071	-0.0293	0.3616	0.1124	0.12	0.1039	-0.003	0.0208	0.1281	0.0709	0.1139	10.835	0.068	-13.318
10	3.4144	-0.4631	0.0941	-0.1584	0.5359	3.2907	-0.0247	0.1149	0.0232	0.2061	0.0428	0.0441	-0.3241	-0.1763	-0.0181	0.0986	-0.0051	0.0511	0.1223	0.0866	0.1352	7.121	12.372	-16.321

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 107
2	X-RAY DIFFRACTION	2	A	108 - 214
3	X-RAY DIFFRACTION	3	B	1 - 114
4	X-RAY DIFFRACTION	4	B	115 - 228
5	X-RAY DIFFRACTION	5	L	1 - 107
6	X-RAY DIFFRACTION	6	L	108 - 214
7	X-RAY DIFFRACTION	7	H	1 - 114
8	X-RAY DIFFRACTION	8	H	115 - 228
9	X-RAY DIFFRACTION	9	V	10 - 116
10	X-RAY DIFFRACTION	10	W	10 - 116

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