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- PDB-6oae: Crystal Structure of Human Mucin-like Protocadherin EC1-2 -

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Basic information

Entry
Database: PDB / ID: 6oae
TitleCrystal Structure of Human Mucin-like Protocadherin EC1-2
ComponentsMucin-like protocadherin
KeywordsCELL ADHESION / brush border morphogenesis / cdhr5 / pcdh24
Function / homology
Function and homology information


intermicrovillar adhesion / regulation of microvillus length / brush border assembly / microvillus membrane / homophilic cell adhesion via plasma membrane adhesion molecules / brush border / microvillus / cell adhesion molecule binding / clathrin-coated pit / brush border membrane ...intermicrovillar adhesion / regulation of microvillus length / brush border assembly / microvillus membrane / homophilic cell adhesion via plasma membrane adhesion molecules / brush border / microvillus / cell adhesion molecule binding / clathrin-coated pit / brush border membrane / beta-catenin binding / cell differentiation / cell adhesion / apical plasma membrane / calcium ion binding / extracellular exosome / plasma membrane
Similarity search - Function
: / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
Mucin-like protocadherin / Cadherin-related family member 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJohnson, Z.R. / Gray, M.E. / Sotomayor, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK095811 United States
CitationJournal: To be published
Title: Crystal Structure of Human Mucin-like Protocadherin EC1-2
Authors: Gray, M.E. / Johnson, Z.R. / Modak, D. / Sotomayor, M.
History
DepositionMar 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Nov 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: Mucin-like protocadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6455
Polymers24,4021
Non-polymers2424
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, bead aggregation assay, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.427, 78.379, 121.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-493-

HOH

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Components

#1: Protein Mucin-like protocadherin


Mass: 24402.199 Da / Num. of mol.: 1 / Fragment: residues 26-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUPCDH / Plasmid: pET21a+ / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): CodonPlus (DE3)-RIPL / References: UniProt: Q58EZ6, UniProt: Q9HBB8*PLUS
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.4 / Details: 0.1M Sodium Acetate pH 4.4, 0.7M Calcium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 19398 / % possible obs: 99.7 % / Redundancy: 24.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 46.14
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 21.8 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 14.5 / Num. unique obs: 943 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UZ8

5uz8


Resolution: 1.9→46.61 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.061 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.142 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23414 948 4.9 %RANDOM
Rwork0.197 ---
obs0.19887 18379 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.323 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å2-0 Å2-0 Å2
2--4.14 Å20 Å2
3----2.69 Å2
Refinement stepCycle: 1 / Resolution: 1.9→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1616 0 11 128 1755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131703
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171543
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.6522337
X-RAY DIFFRACTIONr_angle_other_deg1.2531.5683600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3575215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.79323.93999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60815280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.281510
X-RAY DIFFRACTIONr_chiral_restr0.060.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021925
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5512.913831
X-RAY DIFFRACTIONr_mcbond_other1.5432.908829
X-RAY DIFFRACTIONr_mcangle_it2.5224.3521040
X-RAY DIFFRACTIONr_mcangle_other2.5224.3541041
X-RAY DIFFRACTIONr_scbond_it2.0033.138870
X-RAY DIFFRACTIONr_scbond_other2.0023.14871
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2414.6171292
X-RAY DIFFRACTIONr_long_range_B_refined4.75733.3031767
X-RAY DIFFRACTIONr_long_range_B_other4.71633.0931743
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 66 -
Rwork0.209 1305 -
obs--97.65 %

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