[English] 日本語
Yorodumi
- PDB-1zt5: C-terminal domain of Insulin-like Growth Factor Binding Protein-1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zt5
TitleC-terminal domain of Insulin-like Growth Factor Binding Protein-1 isolated from human amniotic fluid complexed with Iron(II)
ComponentsInsulin-like growth factor binding protein 1
KeywordsPEPTIDE BINDING PROTEIN / Insulin-like Growth Factor Binding Protein-1 / IGFBP-1 / amniotic fluid / C-terminal domain / metal-binding / iron
Function / homology
Function and homology information


regulation of insulin-like growth factor receptor signaling pathway / insulin-like growth factor binding / ATF4 activates genes in response to endoplasmic reticulum stress / tissue regeneration / insulin-like growth factor II binding / insulin-like growth factor I binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway / response to organic cyclic compound ...regulation of insulin-like growth factor receptor signaling pathway / insulin-like growth factor binding / ATF4 activates genes in response to endoplasmic reticulum stress / tissue regeneration / insulin-like growth factor II binding / insulin-like growth factor I binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway / response to organic cyclic compound / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / insulin receptor signaling pathway / positive regulation of cell growth / endoplasmic reticulum lumen / signaling receptor binding / Golgi apparatus / signal transduction / extracellular space / extracellular region
Similarity search - Function
Insulin-like growth factor-binding protein 1 / Thyroglobulin type-1 / Invariant Chain; Chain I / Insulin-like growth factor-binding protein family 1-6, chordata / Insulin-like growth factor binding protein, N-terminal, Cys-rich conserved site / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain signature. / Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues ...Insulin-like growth factor-binding protein 1 / Thyroglobulin type-1 / Invariant Chain; Chain I / Insulin-like growth factor-binding protein family 1-6, chordata / Insulin-like growth factor binding protein, N-terminal, Cys-rich conserved site / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain signature. / Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / Growth factor receptor cysteine-rich domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / : / Insulin-like growth factor-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.818 Å
AuthorsSala, A. / Capaldi, S. / Campagnoli, M. / Faggion, B. / Labo, S. / Perduca, M. / Romano, A. / Carrizo, M.E. / Valli, M. / Visai, L. ...Sala, A. / Capaldi, S. / Campagnoli, M. / Faggion, B. / Labo, S. / Perduca, M. / Romano, A. / Carrizo, M.E. / Valli, M. / Visai, L. / Minchiotti, L. / Galliano, M. / Monaco, H.L.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure and Properties of the C-terminal Domain of Insulin-like Growth Factor-binding Protein-1 Isolated from Human Amniotic Fluid
Authors: Sala, A. / Capaldi, S. / Campagnoli, M. / Faggion, B. / Labo, S. / Perduca, M. / Romano, A. / Carrizo, M.E. / Valli, M. / Visai, L. / Minchiotti, L. / Galliano, M. / Monaco, H.L.
History
DepositionMay 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Insulin-like growth factor binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3293
Polymers9,1851
Non-polymers1442
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.210, 59.600, 31.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Insulin-like growth factor binding protein 1 / IGFBP-1 / IBP- 1 / IGF-binding protein 1 / Placental protein 12 / PP12


Mass: 9185.340 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Source method: isolated from a natural source / Details: Amniotic fluid / Source: (natural) Homo sapiens (human) / References: UniProt: P08833
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: dioxane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 14, 2004 / Details: Double Crystal (Si111, Si220) or White Beam
RadiationMonochromator: Three-segment Pt-coated toroidal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.818→22.34 Å / Num. all: 6773 / Num. obs: 6773 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.48 % / Rsym value: 0.044 / Net I/σ(I): 8.9
Reflection shellResolution: 1.818→1.88 Å / Mean I/σ(I) obs: 5.6 / Rsym value: 0.085 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
XFITdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.818→22.34 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.231 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26425 310 4.7 %RANDOM
Rwork0.22153 ---
all0.232 6577 --
obs0.22333 6267 97.15 %-
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: 24.253 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2---0.68 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.818→22.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms642 0 7 61 710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022669
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.958905
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.472579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.46623.93933
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75515110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.326155
X-RAY DIFFRACTIONr_chiral_restr0.0790.286
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02529
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.2285
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.2457
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7791.5412
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2522642
X-RAY DIFFRACTIONr_scbond_it1.753305
X-RAY DIFFRACTIONr_scangle_it2.7294.5263
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.818→1.865 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 22 -
Rwork0.229 439 -
obs--97.67 %

+
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