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- PDB-3ffd: Structure of parathyroid hormone-related protein complexed to a n... -

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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 / cytoplasm / cytosol
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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: 2.59 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

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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

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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 %

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