[English] 日本語
Yorodumi
- PDB-8t5f: De novo design of high-affinity protein binders to bioactive heli... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8t5f
TitleDe novo design of high-affinity protein binders to bioactive helical peptides
ComponentsParathyroid hormone
KeywordsDE NOVO PROTEIN / Alpha-helical peptides / protein design / diffusion / deep learning
Function / homology
Function and homology information


parathyroid hormone receptor binding / type 1 parathyroid hormone receptor binding / negative regulation of bone mineralization involved in bone maturation / negative regulation of apoptotic process in bone marrow cell / positive regulation of osteoclast proliferation / response to parathyroid hormone / macromolecule biosynthetic process / hormone-mediated apoptotic signaling pathway / positive regulation of cell proliferation in bone marrow / positive regulation of signal transduction ...parathyroid hormone receptor binding / type 1 parathyroid hormone receptor binding / negative regulation of bone mineralization involved in bone maturation / negative regulation of apoptotic process in bone marrow cell / positive regulation of osteoclast proliferation / response to parathyroid hormone / macromolecule biosynthetic process / hormone-mediated apoptotic signaling pathway / positive regulation of cell proliferation in bone marrow / positive regulation of signal transduction / magnesium ion homeostasis / response to fibroblast growth factor / phosphate ion homeostasis / cAMP metabolic process / response to vitamin D / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / positive regulation of inositol phosphate biosynthetic process / peptide hormone receptor binding / bone mineralization / Rho protein signal transduction / positive regulation of glycogen biosynthetic process / bone resorption / positive regulation of bone mineralization / response to cadmium ion / homeostasis of number of cells within a tissue / skeletal system development / positive regulation of D-glucose import / response to lead ion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / intracellular calcium ion homeostasis / cell-cell signaling / regulation of gene expression / G alpha (s) signalling events / response to ethanol / transcription by RNA polymerase II / receptor ligand activity / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / negative regulation of gene expression / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Parathyroid hormone / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsTorres, S.V. / Leung, P.J.Y. / Bera, A.K. / Baker, D. / Kang, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2024
Title: De novo design of high-affinity binders of bioactive helical peptides.
Authors: Vazquez Torres, S. / Leung, P.J.Y. / Venkatesh, P. / Lutz, I.D. / Hink, F. / Huynh, H.H. / Becker, J. / Yeh, A.H. / Juergens, D. / Bennett, N.R. / Hoofnagle, A.N. / Huang, E. / MacCoss, M.J. ...Authors: Vazquez Torres, S. / Leung, P.J.Y. / Venkatesh, P. / Lutz, I.D. / Hink, F. / Huynh, H.H. / Becker, J. / Yeh, A.H. / Juergens, D. / Bennett, N.R. / Hoofnagle, A.N. / Huang, E. / MacCoss, M.J. / Exposit, M. / Lee, G.R. / Bera, A.K. / Kang, A. / De La Cruz, J. / Levine, P.M. / Li, X. / Lamb, M. / Gerben, S.R. / Murray, A. / Heine, P. / Korkmaz, E.N. / Nivala, J. / Stewart, L. / Watson, J.L. / Rogers, J.M. / Baker, D.
History
DepositionJun 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Parathyroid hormone
B: Parathyroid hormone
A: Parathyroid hormone


Theoretical massNumber of molelcules
Total (without water)12,3773
Polymers12,3773
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-23 kcal/mol
Surface area8800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.324, 91.324, 37.732
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11C-209-

HOH

-
Components

#1: Protein/peptide Parathyroid hormone / PTH / Parathormone / Parathyrin


Mass: 4125.778 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01270
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.4 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M Sodium chloride, 0.1 M Sodium acetate pH 4.5, and 1.26 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.99→40.84 Å / Num. obs: 11302 / % possible obs: 98.6 % / Redundancy: 15.1 % / Biso Wilson estimate: 46.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Net I/σ(I): 21.8
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 738 / CC1/2: 0.545 / % possible all: 94.6

-
Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→40.84 Å / SU ML: 0.2581 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 30.6883
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2508 518 4.85 %
Rwork0.2191 10163 -
obs0.2206 10681 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.17 Å2
Refinement stepCycle: LAST / Resolution: 1.99→40.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms853 0 0 26 879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01867
X-RAY DIFFRACTIONf_angle_d1.04281157
X-RAY DIFFRACTIONf_chiral_restr0.058125
X-RAY DIFFRACTIONf_plane_restr0.0089145
X-RAY DIFFRACTIONf_dihedral_angle_d4.0545104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.190.33851270.25032200X-RAY DIFFRACTION83.58
2.19-2.50.28851150.24672490X-RAY DIFFRACTION92.28
2.5-3.150.28131350.2462648X-RAY DIFFRACTION96.93
3.15-40.840.22881410.20372825X-RAY DIFFRACTION98.28
Refinement TLS params.Method: refined / Origin x: 16.9886687926 Å / Origin y: 56.4334783352 Å / Origin z: 4.06471552646 Å
111213212223313233
T0.284035269491 Å2-0.0259847373699 Å20.00473141224426 Å2-0.336597749641 Å20.00187316835531 Å2--0.289396042273 Å2
L1.30742790368 °21.07487677905 °20.637990173755 °2-2.41904997759 °2-0.228715007551 °2--0.656237068851 °2
S-0.0478234626789 Å °0.0708078845132 Å °-0.0656247618412 Å °-0.108160434031 Å °0.0296762516175 Å °-0.0301684395001 Å °-0.032926559384 Å °0.162160663443 Å °0.0250697335428 Å °
Refinement TLS groupSelection details: all

+
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