[English] 日本語
Yorodumi
- PDB-3ffd: Structure of parathyroid hormone-related protein complexed to a n... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ffd
TitleStructure of parathyroid hormone-related protein complexed to a neutralizing monoclonal antibody
Components
  • Monoclonal antibody, heavy chain, Fab fragment
  • Monoclonal antibody, light chain, Fab fragment
  • Parathyroid hormone-related protein
KeywordsIMMUNE SYSTEM/HORMONE / pthrp complexed to fab / Cleavage on pair of basic residues / Hormone / Nucleus / Secreted / IMMUNE SYSTEM-HORMONE COMPLEX
Function / homology
Function and homology information


negative regulation of chondrocyte development / regulation of chondrocyte differentiation / cAMP metabolic process / Class B/2 (Secretin family receptors) / negative regulation of chondrocyte differentiation / osteoblast development / peptide hormone receptor binding / bone mineralization / epidermis development / skeletal system development ...negative regulation of chondrocyte development / regulation of chondrocyte differentiation / cAMP metabolic process / Class B/2 (Secretin family receptors) / negative regulation of chondrocyte differentiation / osteoblast development / peptide hormone receptor binding / bone mineralization / epidermis development / skeletal system development / female pregnancy / hormone activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell-cell signaling / regulation of gene expression / G alpha (s) signalling events / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Golgi apparatus / extracellular space / extracellular region / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Parathyroid hormone-related protein / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Parathyroid hormone-related protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMckinstry, W.J. / Polekhina, G. / Diefenbach-Jagger, H. / Ho, P.W.M. / Sato, K. / Onuma, E. / Gillespie, M.T. / Martin, T.J. / Parker, M.W.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Structural basis for antibody discrimination between two hormones that recognize the parathyroid hormone receptor
Authors: McKinstry, W.J. / Polekhina, G. / Diefenbach-Jagger, H. / Ho, P.W.M. / Sato, K. / Onuma, E. / Gillespie, M.T. / Martin, T.J. / Parker, M.W.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Multiple sites of contact between the carboxyl-terminal binding domain of PTHrP-(1--36) analogs and the amino-terminal extracellular domain of the PTH/PTHrP receptor identified by photoaffinity cross-linking
Authors: Gensure, R.C. / Gardella, T.J. / Juppner, H.
#2: Journal: Trends Endocrinol.Metab. / Year: 2001
Title: Molecular properties of the PTH/PTHrP receptor
Authors: Gardella, T.J. / Juppner, H.
History
DepositionDec 3, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Monoclonal antibody, heavy chain, Fab fragment
B: Monoclonal antibody, light chain, Fab fragment
P: Parathyroid hormone-related protein


Theoretical massNumber of molelcules
Total (without water)59,6893
Polymers59,6893
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-29 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.613, 96.285, 88.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Antibody Monoclonal antibody, heavy chain, Fab fragment


Mass: 23340.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma cell
Cellular location (production host): abdominal cavity of balb/c
Production host: mus musculus (house mouse)
#2: Antibody Monoclonal antibody, light chain, Fab fragment


Mass: 23751.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma cell
Cellular location (production host): abdominal cavity of balb/c
Production host: mus musculus (house mouse)
#3: Protein Parathyroid hormone-related protein / PTH-rP / PTHrP


Mass: 12597.367 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) / References: UniProt: P12272
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: PEG 400, TRIS, pH 8.70, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 / Wavelength: 0.99988 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 3, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.999881
ReflectionResolution: 2→30 Å / Num. all: 42014 / Num. obs: 42012 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 29.03 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 27.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 8 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 4.1 / Num. unique all: 4138 / Rsym value: 0.696 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IGT AND 1IGC

1igt

1igc


Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 4235 -RANDOM
Rwork0.224 ---
obs0.224 42012 99.2 %-
all-42012 --
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 0 204 3595
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_improper_angle_d1.14
LS refinement shellResolution: 2→2.13 Å
RfactorNum. reflection% reflection
Rfree0.339 631 -
Rwork0.332 --
obs--100 %

+
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