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- PDB-7n86: Crystal Structure of Human Protocadherin-24 EC1-2 Form II -

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Basic information

Entry
Database: PDB / ID: 7n86
TitleCrystal Structure of Human Protocadherin-24 EC1-2 Form II
ComponentsCadherin-related family member 2
KeywordsCELL ADHESION / BRUSH BORDER / CALCIUM BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of cell growth involved in contact inhibition / intermicrovillar adhesion / regulation of microvillus length / cell-cell adhesion mediated by cadherin / anchoring junction / microvillus membrane / homophilic cell adhesion via plasma membrane adhesion molecules / brush border / cell adhesion molecule binding / epithelial cell differentiation ...negative regulation of cell growth involved in contact inhibition / intermicrovillar adhesion / regulation of microvillus length / cell-cell adhesion mediated by cadherin / anchoring junction / microvillus membrane / homophilic cell adhesion via plasma membrane adhesion molecules / brush border / cell adhesion molecule binding / epithelial cell differentiation / brush border membrane / apical plasma membrane / calcium ion binding / extracellular exosome / plasma membrane
Similarity search - Function
Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily
Similarity search - Domain/homology
IODIDE ION / Cadherin-related family member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.175 Å
AuthorsModak, D. / 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)R01 DK095811 United States
CitationJournal: Plos Biol. / Year: 2021
Title: Heterophilic and homophilic cadherin interactions in intestinal intermicrovillar links are species dependent.
Authors: Gray, M.E. / Johnson, Z.R. / Modak, D. / Tamilselvan, E. / Tyska, M.J. / Sotomayor, M.
History
DepositionJun 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cadherin-related family member 2
B: Cadherin-related family member 2
C: Cadherin-related family member 2
D: Cadherin-related family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,58432
Polymers104,1694
Non-polymers3,41528
Water59433
1
A: Cadherin-related family member 2
B: Cadherin-related family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,86416
Polymers52,0852
Non-polymers1,77914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-38 kcal/mol
Surface area21010 Å2
MethodPISA
2
C: Cadherin-related family member 2
D: Cadherin-related family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,72016
Polymers52,0852
Non-polymers1,63614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-52 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.899, 86.641, 104.892
Angle α, β, γ (deg.)90.000, 103.458, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74B
84C
95B
105D
116C
126D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: 1

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA1 - 2151 - 215
21PROPROBB1 - 2151 - 215
32ASPASPAA1 - 2131 - 213
42ASPASPCC1 - 2131 - 213
53GLNGLNAA1 - 2141 - 214
63GLNGLNDD1 - 2141 - 214
74ASPASPBB1 - 2131 - 213
84ASPASPCC1 - 2131 - 213
95GLNGLNBB1 - 2141 - 214
105GLNGLNDD1 - 2141 - 214
116ASPASPCC1 - 2131 - 213
126ASPASPDD1 - 2131 - 213

NCS ensembles :
IDDetails
1Global NCS restraints between domains: 1 2
2Global NCS restraints between domains: 3 4
3Global NCS restraints between domains: 5 6
4Global NCS restraints between domains: 7 8
5Global NCS restraints between domains: 9 10
6Global NCS restraints between domains: 11 12

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Cadherin-related family member 2 / Protocadherin LKC / PC-LKC / Protocadherin-24


Mass: 26042.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Cleaved signal peptide (1-20) not included / Source: (gene. exp.) Homo sapiens (human) / Gene: CDHR2, PCDH24, PCLKC / Plasmid: PHIS-N1 / Cell line (production host): EXPI293 / Production host: Homo sapiens (human) / References: UniProt: Q9BYE9
#2: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 57 molecules

#3: 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
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 MM NaI 20% PEG3350 CDHR5 EC1-2

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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: Dec 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.175→50 Å / Num. obs: 18809 / % possible obs: 96.3 % / Redundancy: 3.5 % / CC1/2: 0.987 / Net I/σ(I): 5.6
Reflection shellResolution: 3.175→3.23 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.63 / Num. unique obs: 810 / CC1/2: 0.277 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CZR

5czr


Resolution: 3.175→49.147 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.81 / SU B: 25.538 / SU ML: 0.438 / Cross valid method: FREE R-VALUE / ESU R Free: 0.593
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2896 862 4.767 %
Rwork0.2135 17221 -
all0.217 --
obs-18083 95.219 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.168 Å2
Baniso -1Baniso -2Baniso -3
1--0.375 Å2-0 Å2-1.706 Å2
2--0.913 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 3.175→49.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6500 0 187 33 6720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0136817
X-RAY DIFFRACTIONr_bond_other_d0.0040.0176366
X-RAY DIFFRACTIONr_angle_refined_deg2.021.6659295
X-RAY DIFFRACTIONr_angle_other_deg1.4891.59814703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2315841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53125.069290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.808151054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7861512
X-RAY DIFFRACTIONr_chiral_restr0.0730.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027607
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021441
X-RAY DIFFRACTIONr_nbd_refined0.2440.21069
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2260.25797
X-RAY DIFFRACTIONr_nbtor_refined0.1850.23223
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1080.23763
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2116
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1370.22
X-RAY DIFFRACTIONr_metal_ion_refined0.3130.253
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2970.224
X-RAY DIFFRACTIONr_nbd_other0.3230.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2660.21
X-RAY DIFFRACTIONr_mcbond_it5.4693.9923386
X-RAY DIFFRACTIONr_mcbond_other5.4673.9913385
X-RAY DIFFRACTIONr_mcangle_it8.4665.9794219
X-RAY DIFFRACTIONr_mcangle_other8.4655.984220
X-RAY DIFFRACTIONr_scbond_it7.7664.7463431
X-RAY DIFFRACTIONr_scbond_other7.7664.7463431
X-RAY DIFFRACTIONr_scangle_it11.3866.8495076
X-RAY DIFFRACTIONr_scangle_other11.3856.8515077
X-RAY DIFFRACTIONr_lrange_it15.89979.89326635
X-RAY DIFFRACTIONr_lrange_other15.89979.89526630
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight positional; tight thermal / Weight Biso : 0.86601 / Weight position: 0.0866

Ens-IDDom-IDAuth asym-IDRms dev Biso (Å2)Rms dev position (Å)
11A8.866220.50982
12B8.866220.50982
23A8.281940.63083
24C8.281940.63083
35A7.25430.4381
36D7.25430.4381
47B7.614330.45163
48C7.614330.45163
59B8.546550.56262
510D8.546550.56262
611C8.117020.57889
612D8.117020.57889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.175-3.2570.313570.2351008X-RAY DIFFRACTION77.4545
3.257-3.3460.328710.2331195X-RAY DIFFRACTION92.6794
3.346-3.4430.338660.2351156X-RAY DIFFRACTION93.2824
3.443-3.5490.341750.2321160X-RAY DIFFRACTION94.8541
3.549-3.6650.336540.2311131X-RAY DIFFRACTION96.1851
3.665-3.7930.312520.2141134X-RAY DIFFRACTION97.5329
3.793-3.9360.334460.1881099X-RAY DIFFRACTION98.0308
3.936-4.0970.244320.1851061X-RAY DIFFRACTION98.2914
4.097-4.2790.235460.1771008X-RAY DIFFRACTION97.0534
4.279-4.4870.244420.179947X-RAY DIFFRACTION97.1513
4.487-4.7290.199410.161881X-RAY DIFFRACTION94.4672
4.729-5.0160.208420.152887X-RAY DIFFRACTION98.62
5.016-5.3610.243470.166827X-RAY DIFFRACTION99.3182
5.361-5.7890.298370.186779X-RAY DIFFRACTION99.5122
5.789-6.340.283390.209697X-RAY DIFFRACTION99.0579
6.34-7.0850.302290.226653X-RAY DIFFRACTION98.8406
7.085-8.1740.281290.225555X-RAY DIFFRACTION98.1513
8.174-9.9950.293250.299464X-RAY DIFFRACTION94.9515
9.995-14.0680.363240.334372X-RAY DIFFRACTION97.0588
14.068-49.1470.39480.415207X-RAY DIFFRACTION90.7173

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