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- PDB-3w7z: 1.15A structure of human 2Zn insulin at 293K -

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Basic information

Entry
Database: PDB / ID: 3w7z
Title1.15A structure of human 2Zn insulin at 293K
Components(Insulin) x 2
KeywordsHORMONE / Human insulin / glucose metabolism / secretion
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsHoshikawa, N. / Sasaki, K. / Sakabe, N. / Sakabe, K.
Citation
Journal: To be Published
Title: 1.15A structure of human 2Zn insulin at 293K
Authors: Hoshikawa, N. / Sasaki, K. / Sakabe, N. / Sakabe, K.
#1: Journal: NUCL INSTRUM METHODS PHYS RES A / Year: 2001
Title: Automatic Weissenberg data collection system for time-resolved protein crystallography
Authors: Sakabe, N. / Sakabe, K. / Higashi, T. / Igarashi, N. / Suzuki, M. / Watanabe, N. / Sasaki, K.
#2: Journal: J.SYNCHROTRON RADIAT. / Year: 1999
Title: Rotated-inclined focusing monochromator with simultaneous tuning of asymmetry factor and radius of curvature over a wide wavelength range
Authors: Watanabe, N. / Suzuki, M. / Higashi, Y. / Sakabe, N.
#3: Journal: J.SYNCHROTRON RADIAT. / Year: 1997
Title: Large-Format Imaging Plate and Weissenberg Camera for Accurate Protein Crystallographic Data Collection Using Synchrotron Radiation
Authors: Sakabe, K. / Sasaki, K. / Watanabe, N. / Suzuki, M. / Wang, Z.G. / Miyahara, J. / Sakabe, N.
#4: Journal: PHILOS.TRANS.R.SOC.LOND.B BIOL / Year: 1988
Title: The structure of 2Zn pig insulin crystals at 1.5A resolution
Authors: Baker, E. / Blundell, T.L. / Cutfield, J.F. / Cutfield, S.M. / Dodson, E.J. / Dodson, G. / Hodgkin, D.M.C. / Hubbard, E. / Isaacs, N.W. / Reynolds, C.D. / Sakabe, K. / Sakabe, N. / Vijayan, N.M.
#5: Journal: Acta Crystallogr.,Sect.A / Year: 1972
Title: A statistical evaluation of absorption
Authors: Katayama, C. / Sakabe, N. / Sakabe, K.
#6: Journal: J.APPL.CRYSTALLOGR. / Year: 1989
Title: The processing of diffraction data taken on a screenless Weissenberg camera for macromolecular crystallography
Authors: Higashi, T.
History
DepositionMar 11, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin
B: Insulin
C: Insulin
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7666
Polymers11,6354
Non-polymers1312
Water4,648258
1
A: Insulin
B: Insulin
hetero molecules

A: Insulin
B: Insulin
hetero molecules

A: Insulin
B: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6499
Polymers17,4536
Non-polymers1963
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5590 Å2
ΔGint-96 kcal/mol
Surface area10850 Å2
MethodPISA
2
C: Insulin
D: Insulin
hetero molecules

C: Insulin
D: Insulin
hetero molecules

C: Insulin
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6499
Polymers17,4536
Non-polymers1963
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5330 Å2
ΔGint-92 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.700, 82.700, 34.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-501-

ZN

21D-501-

ZN

31D-632-

HOH

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Components

#1: Protein/peptide Insulin / / Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: UNP residues 90-110 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide Insulin / / Insulin B chain


Mass: 3433.953 Da / Num. of mol.: 2 / Fragment: UNP residues 25-54 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.67
Details: 10mg/ml protein, 0.1M Sodium Citrate, 22%(v/v) DMF, 0.08%(w/v) Zinc chloride, pH 8.67, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6C / Wavelength: 1 Å
DetectorType: Fully automatic high speed Weissenberg data collection system called Galaxy
Detector: IMAGE PLATE / Date: Apr 13, 2002
Details: The vertically focusing 1m long bent mirror of Pt-coated fused silica is 21m from the SR source point and 7m from the focus point
RadiationMonochromator: Rotated-inclined focusing S(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→41.5 Å / Num. obs: 46687 / Redundancy: 8.4 % / Rmerge(I) obs: 0.066

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Processing

Software
NameVersionClassification
WEISdata scaling
CCP4model building
REFMAC5.7.0032refinement
WEISdata reduction
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W7Y

3w7y


Resolution: 1.15→20 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.286 / SU ML: 0.027 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 1556 5 %RANDOM
Rwork0.14509 ---
obs0.14767 29333 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.135 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.03 Å20 Å2
2--0.03 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 2 258 1070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.019832
X-RAY DIFFRACTIONr_angle_refined_deg1.0571.9541130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.386598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.63424.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.66815130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.743152
X-RAY DIFFRACTIONr_chiral_restr0.0820.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02636
X-RAY DIFFRACTIONr_rigid_bond_restr1.4923832
X-RAY DIFFRACTIONr_sphericity_free44.099544
X-RAY DIFFRACTIONr_sphericity_bonded24.52951026
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 113 -
Rwork0.275 2146 -
obs-2146 97.71 %

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