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- PDB-1sgf: CRYSTAL STRUCTURE OF 7S NGF: A COMPLEX OF NERVE GROWTH FACTOR WIT... -

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Basic information

Entry
Database: PDB / ID: 1sgf
TitleCRYSTAL STRUCTURE OF 7S NGF: A COMPLEX OF NERVE GROWTH FACTOR WITH FOUR BINDING PROTEINS (SERINE PROTEINASES)
Components(NERVE GROWTH ...) x 3
KeywordsGROWTH FACTOR / GROWTH FACTOR (BETA-NGF) / HYDROLASE - SERINE PROTEINASE (GAMMA-NGF) / INACTIVE SERINE PROTEINASE (ALPHA-NGF)
Function / homology
Function and homology information


TRKA activation by NGF / NFG and proNGF binds to p75NTR / NADE modulates death signalling / NGF processing / tissue kallikrein / Axonal growth stimulation / Activation of Matrix Metalloproteinases / : / Frs2-mediated activation / negative regulation of type B pancreatic cell apoptotic process ...TRKA activation by NGF / NFG and proNGF binds to p75NTR / NADE modulates death signalling / NGF processing / tissue kallikrein / Axonal growth stimulation / Activation of Matrix Metalloproteinases / : / Frs2-mediated activation / negative regulation of type B pancreatic cell apoptotic process / positive regulation of neurotrophin TRK receptor signaling pathway / PI3K/AKT activation / ARMS-mediated activation / nerve growth factor receptor binding / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / Retrograde neurotrophin signalling / NF-kB is activated and signals survival / positive regulation of neuron maturation / metalloendopeptidase inhibitor activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / nerve growth factor signaling pathway / regulation of neurotransmitter secretion / nerve development / regulation of systemic arterial blood pressure / positive regulation of collateral sprouting / peripheral nervous system development / regulation of release of sequestered calcium ion into cytosol / axon extension / positive regulation of Ras protein signal transduction / zymogen activation / regulation of neuron differentiation / small GTPase-mediated signal transduction / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of stem cell proliferation / positive regulation of axon extension / positive regulation of DNA binding / positive regulation of protein autophosphorylation / extrinsic apoptotic signaling pathway in absence of ligand / sensory perception of pain / positive regulation of neuron differentiation / adult locomotory behavior / neuron projection morphogenesis / secretory granule / positive regulation of protein ubiquitination / endosome lumen / cell surface receptor protein tyrosine kinase signaling pathway / growth factor activity / modulation of chemical synaptic transmission / memory / positive regulation of neuron projection development / circadian rhythm / neuron projection development / synaptic vesicle / positive regulation of peptidyl-serine phosphorylation / positive regulation of cell growth / neuron apoptotic process / endopeptidase activity / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / axon / serine-type endopeptidase activity / lipid binding / dendrite / positive regulation of cell population proliferation / positive regulation of gene expression / protein-containing complex / extracellular space / extracellular region / metal ion binding
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 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Kallikrein 1-related peptidase b3 / Kallikrein 1-related peptidase-like b4 / Beta-nerve growth factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsBax, B.D.V. / Blundell, T.L. / Murray-Rust, J. / Mcdonald, N.Q.
Citation
Journal: Structure / Year: 1997
Title: Structure of mouse 7S NGF: a complex of nerve growth factor with four binding proteins.
Authors: Bax, B. / Blundell, T.L. / Murray-Rust, J. / McDonald, N.Q.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization and Characterization of the High Molecular Weight Form of Nerve Growth Factor (7 S Ngf)
Authors: Mcdonald, N.Q. / Blundell, T.L.
History
DepositionAug 8, 1997Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / diffrn_source / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / software / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NERVE GROWTH FACTOR
B: NERVE GROWTH FACTOR
G: NERVE GROWTH FACTOR
X: NERVE GROWTH FACTOR
Y: NERVE GROWTH FACTOR
Z: NERVE GROWTH FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,40712
Polymers132,9856
Non-polymers1,4226
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15560 Å2
ΔGint-128 kcal/mol
Surface area45250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.680, 96.590, 147.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9651, 0.25022, 0.07734), (0.2502, 0.79363, 0.55458), (0.07739, 0.55457, -0.82853)
Vector: 21.57266, 0.10399, -10.07073)

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Components

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NERVE GROWTH ... , 3 types, 6 molecules AXBYGZ

#1: Protein NERVE GROWTH FACTOR / / 7S NGF


Mass: 26783.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: MALE SUBMANDIBULAR GLAND / Strain: SWISS WEBSTER / References: UniProt: P00757, tissue kallikrein
#2: Protein NERVE GROWTH FACTOR / / 7S NGF


Mass: 13277.009 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: MALE SUBMANDIBULAR GLAND / Strain: SWISS WEBSTER / References: UniProt: P01139, tissue kallikrein
#3: Protein NERVE GROWTH FACTOR / / 7S NGF


Mass: 26432.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: MALE SUBMANDIBULAR GLAND / Strain: SWISS WEBSTER / References: UniProt: P00756, tissue kallikrein

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Sugars , 2 types, 4 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 2 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Compound detailsAN INTERNAL CLEAVAGE SITE EXISTS IN THE 'KALLIKREIN LOOP' OF THE GAMMA-NGF SUBUNITS WHICH RESULTS ...AN INTERNAL CLEAVAGE SITE EXISTS IN THE 'KALLIKREIN LOOP' OF THE GAMMA-NGF SUBUNITS WHICH RESULTS IN THE REMOVAL OF FOUR RESIDUES (G 95F - G 95I, Z 95F - Z 95I). 7S NGF (HIGH MOLECULAR WEIGHT FORM OF NERVE GROWTH FACTOR). 7S NGF CAN BE DISSOCIATED INTO THE BETA-NGF DIMER, THE ACTIVE NEUROTROPHIN, AND MONOMERIC ALPHA-NGF AND GAMMA-NGF. ALPHA-NGF AND GAMMA-NGF ARE CLOSELY RELATED MEMBERS OF THE GLANDULAR KALLIKREIN FAMILY OF SERINE PROTEINASES. GAMMA-NGF IS AN ACTIVE SERINE PROTEINASE, ALPHA-NGF IS INACTIVE. THE STOICHIOMETRY OF THE COMPLEX IS ALPHA2BETA2GAMMA2.
Sequence detailsTHE RESIDUE NOMENCLATURE FOR THE ALPHA AND GAMMA SUBUNITS IS BASED ON THEIR ALIGNMENT WITH ...THE RESIDUE NOMENCLATURE FOR THE ALPHA AND GAMMA SUBUNITS IS BASED ON THEIR ALIGNMENT WITH CHYMOTRYPSINOGEN. THE ALPHA NGF SUBUNITS ARE DISORDERED IN THREE REGIONS: AT THE N-TERMINUS (A 9 - A 24, X 9 - X 25), IN THE '70S LOOP' (A 71 - A 77, X 71 - X 79A), AND IN THE 'AUTOLYSIS LOOP' (A 140 - A 156, X 141 - X 156). AMINO ACID SEQUENCING HAS SHOWN THERE IS A CLEAVAGE SITE IN THE 'AUTOLYSIS LOOP'.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53 % / Description: DATA ARE VERY ANISOTROPIC
Crystal growpH: 4.9
Details: PROTEIN WAS CRYSTALLIZED FROM 20MG/ML PROTEIN SOLUTION IN 50MM SODIUM PHOSPHATE (PH6.8) MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION (50MM SODIUM ACETATE PH4.5-5.1, 12-21% PEG 4000, 10 ...Details: PROTEIN WAS CRYSTALLIZED FROM 20MG/ML PROTEIN SOLUTION IN 50MM SODIUM PHOSPHATE (PH6.8) MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION (50MM SODIUM ACETATE PH4.5-5.1, 12-21% PEG 4000, 10 MICROMOLAR ZNSO4) (MCDONALD AND BLUNDELL, 1991, JMB, 219, 595-601)., pH 4.9
PH range: 5.0-5.1
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mMsodium phosphate1drop
350 mMsodium acetate1reservoir
40.01 M1reservoirZnSO4
512-16 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Type: EMBL/DESY, HAMBURG / Wavelength: 0.96
DetectorDetector: IMAGE PLATE / Date: May 1, 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 24209 / % possible obs: 96 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 10.5
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.427 / % possible all: 92.5
Reflection shell
*PLUS
% possible obs: 92.5 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATA/AGROVATAdata reduction
TFFCmodel building
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TFFCphasing
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BETA-NGF AND PORCINE PANCREATIC KALLIKREIN (1BET AND 2PKA)

1bet

2pka


Resolution: 3.15→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1
Isotropic thermal model: ONE MAIN CHAIN AND ONE SI CHAIN TEMPERATURE FACTOR WERE REFINED PER RESIDUE
Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.282 612 2.5 %THIN SHELLS
Rwork0.246 ---
obs0.246 21857 97 %-
Displacement parametersBiso mean: 40.9 Å2
Baniso -1Baniso -2Baniso -3
1--43.24 Å20 Å20 Å2
2---0.47 Å20 Å2
3----0.06 Å2
Refine analyzeLuzzati d res low obs: 4.5 Å / Luzzati sigma a obs: 0.52 Å
Refinement stepCycle: LAST / Resolution: 3.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8463 0 86 0 8549
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.75
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.51
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3.15→3.28 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3601 51 2 %
Rwork0.3623 2551 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_BEN96P.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PAR_NAGZN.PARTOP_NAGZNMAN_SER195.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.51
LS refinement shell
*PLUS
Rfactor obs: 0.3623

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