[English] 日本語
Yorodumi
- PDB-4edw: Nerve Growth Factor in Complex with Fab from humanized version of... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4edw
TitleNerve Growth Factor in Complex with Fab from humanized version of mouse mAb 911 (tanezumab)
Components
  • Beta-nerve growth factor
  • tanezumab Fab heavy chain
  • tanezumab Fab light chain
KeywordsIMMUNE 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 ...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 / Retrograde neurotrophin signalling / nerve development / Axonal growth stimulation / positive regulation of collateral sprouting / NADE modulates death signalling / Signalling to p38 via RIT and RIN / peripheral nervous system development / ARMS-mediated activation / positive regulation of Ras protein signal transduction / PI3K/AKT activation / regulation of neuron differentiation / Frs2-mediated activation / NRAGE signals death through JNK / extrinsic apoptotic signaling pathway via death domain receptors / Signalling to RAS / positive regulation of DNA binding / p75NTR recruits signalling complexes / positive regulation of neuron differentiation / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / neuron projection morphogenesis / endosome lumen / growth factor activity / modulation of chemical synaptic transmission / memory / Golgi lumen / cell surface receptor protein tyrosine kinase signaling pathway / synaptic vesicle / positive regulation of peptidyl-serine phosphorylation / negative regulation of neuron apoptotic process / axon / negative regulation of cell population proliferation / dendrite / lipid binding / positive regulation of gene expression / extracellular space / extracellular region / cytosol
Similarity search - Function
Nerve growth factor, beta subunit, mammalian / Nerve growth factor, beta subunit / Nerve growth factor family profile. / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like / Nerve growth factor family / Nerve growth factor family signature. / Nerve growth factor (NGF or beta-NGF) / Cystine Knot Cytokines, subunit B ...Nerve growth factor, beta subunit, mammalian / Nerve growth factor, beta subunit / Nerve growth factor family profile. / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like / Nerve growth factor family / Nerve growth factor family signature. / Nerve growth factor (NGF or beta-NGF) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-nerve growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsEigenbrot, C. / Ultsch, M.
CitationJournal: 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
DepositionMar 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Oct 25, 2017Group: Advisory / Derived calculations / Refinement description
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
V: Beta-nerve growth factor
L: tanezumab Fab light chain
H: tanezumab Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1884
Polymers62,0963
Non-polymers921
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-31 kcal/mol
Surface area25550 Å2
Unit cell
Length a, b, c (Å)64.700, 92.707, 252.729
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Beta-nerve growth factor / Beta-NGF


Mass: 13515.410 Da / Num. of mol.: 1
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 tanezumab Fab light chain


Mass: 23621.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody tanezumab Fab heavy chain


Mass: 24959.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.69 %
Crystal growTemperature: 300 K / pH: 6.8
Details: PEG 5000 monomethylether, glycerol, sodium cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 300K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 8, 2005
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 25872 / % possible obs: 95.2 % / Observed criterion σ(I): -2 / Redundancy: 6.6 % / Biso Wilson estimate: 62.52 Å2 / Rsym value: 0.062 / Net I/σ(I): 24

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→45.59 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.8736 / SU B: 9.534 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.397 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 1320 5.12 %RANDOM
Rwork0.2002 ---
obs0.2026 25793 93.94 %-
all-24244 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 69.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.0702 Å20 Å20 Å2
2---29.8352 Å20 Å2
3---29.9054 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.48→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4128 0 6 37 4171
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.009
X-RAY DIFFRACTIONt_angle_deg1.26
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 2.48→2.58 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.404 111 5.48 %
Rwork0.2464 1914 -
all0.2544 2025 -
obs--93.94 %
Refinement TLS params.

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

IDL11 (°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)
11.06960.8617-1.05033.0207-0.87754.8625-0.0290.15070.0438-0.13520.05140.2820.5347-0.8387-0.02240.1396-0.1373-0.0830.2736-0.00450.1634-12.574-26.637-39.147
21.32030.5788-0.33752.14980.11713.847-0.0653-0.1806-0.1086-0.05680.06930.0240.03970.0732-0.0040.0738-0.0116-0.01760.19650.03390.1828-8.592-32.405-2.235
30.1129-0.13420.04951.47430.93896.4524-0.05290.02390.1033-0.00570.1836-0.0455-0.90230.0601-0.13080.251-0.0057-0.01520.1291-0.03480.1624-2.236-8.037-34.737
43.7643-0.2092-0.02012.4666-0.92224.64520.0970.0342-0.25630.1975-0.2019-0.21740.03360.24950.10490.0455-0.0352-0.01980.1752-0.03550.13463.701-23.556-8.728
51.52881.8341-0.5124.1246-0.65953.74320.1362-0.19550.02440.023-0.1382-0.009-0.17070.59420.0020.2275-0.0466-0.01270.2978-0.03380.17686.41-12.945-62.992
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 107
2X-RAY DIFFRACTION2L108 - 214
3X-RAY DIFFRACTION3H1 - 112
4X-RAY DIFFRACTION4H113 - 213
5X-RAY DIFFRACTION5V10 - 115

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more