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- PDB-5czr: Crystal Structure of Human Protocadherin-24 EC1-2 -

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Basic information

Entry
Database: PDB / ID: 5czr
TitleCrystal Structure of Human Protocadherin-24 EC1-2
ComponentsCadherin-related family member 2
KeywordsCELL ADHESION / adhesion / brush border
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 / epithelial cell differentiation / cell adhesion molecule binding ...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 / epithelial cell differentiation / cell adhesion molecule binding / brush border membrane / apical plasma membrane / calcium ion binding / extracellular exosome / plasma membrane
Similarity search - Function
Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like ...Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cadherin-related family member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJohnson, Z.R. / Sotomayor, M.
CitationJournal: To Be Published
Title: Crystal Structure of Human Protocadherin-24 EC1-2
Authors: Johnson, Z.R. / Sotomayor, M.
History
DepositionAug 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)99,66920
Polymers99,0284
Non-polymers64116
Water4,288238
1
A: Cadherin-related family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9175
Polymers24,7571
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cadherin-related family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9175
Polymers24,7571
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cadherin-related family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9175
Polymers24,7571
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cadherin-related family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9175
Polymers24,7571
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.879, 119.769, 74.318
Angle α, β, γ (deg.)90.00, 104.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNGLNGLNAA1 - 2142 - 215
21ASNASNGLNGLNBB1 - 2142 - 215
12ASNASNGLNGLNAA1 - 2142 - 215
22ASNASNGLNGLNCC1 - 2142 - 215
13ASNASNGLNGLNAA1 - 2142 - 215
23ASNASNGLNGLNDD1 - 2142 - 215
14ASNASNGLNGLNBB1 - 2142 - 215
24ASNASNGLNGLNCC1 - 2142 - 215
15METMETPROPROBB0 - 2151 - 216
25METMETPROPRODD0 - 2151 - 216
16ASNASNGLNGLNCC1 - 2142 - 215
26ASNASNGLNGLNDD1 - 2142 - 215

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 24756.947 Da / Num. of mol.: 4 / Fragment: Cadherin domains 1 and 2 residues 21-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDHR2, PCDH24, PCLKC / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BYE9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 0.2 M MgCl 0.1 M HEPES pH 7.3 10% PEF 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 50945 / % possible obs: 95.5 % / Redundancy: 3.1 % / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 3 / % possible all: 80.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CYX

5cyx


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.556 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23546 2458 4.8 %RANDOM
Rwork0.20463 ---
obs0.20617 48462 95.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.633 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å2-0.32 Å2
2--0.3 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6610 0 16 238 6864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026758
X-RAY DIFFRACTIONr_bond_other_d0.0060.026342
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9629225
X-RAY DIFFRACTIONr_angle_other_deg1.23314624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3115859
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.90625.789285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.835151065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1461512
X-RAY DIFFRACTIONr_chiral_restr0.0850.21087
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217693
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021467
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_it2.0562.8463448
X-RAY DIFFRACTIONr_mcbond_other2.0522.8453447
X-RAY DIFFRACTIONr_mcangle_it3.3374.2574303
X-RAY DIFFRACTIONr_mcangle_other3.3374.2594304
X-RAY DIFFRACTIONr_scbond_it2.3423.113310
X-RAY DIFFRACTIONr_scbond_other2.3423.1113311
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7974.5524923
X-RAY DIFFRACTIONr_long_range_B_refined5.7822.4787146
X-RAY DIFFRACTIONr_long_range_B_other5.77522.4347098
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A244900.08
12B244900.08
21A240500.09
22C240500.09
31A235940.09
32D235940.09
41B243580.09
42C243580.09
51B240060.1
52D240060.1
61C239000.09
62D239000.09
LS refinement shellResolution: 2.299→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 147 -
Rwork0.278 2915 -
obs--77.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
11.24381.1513-1.03151.2218-1.0810.97790.2419-0.07190.04520.1876-0.15120.0486-0.18950.1222-0.09080.1269-0.01860.06970.0646-0.00710.1151AEC1 Protein-36.676-157.448181.169
20.32970.6423-0.66051.7383-1.1041.604-0.0626-0.0157-0.0265-0.18630.0772-0.0403-0.01140.0064-0.01460.1183-0.00220.09410.0612-0.00810.0983AEC2 Protein-15.425-131.773146.942
31.0753-0.4451-0.45770.2830.37640.5520.09190.02580.0047-0.0555-0.0394-0.0321-0.0605-0.056-0.05250.16390.04230.13970.02250.03680.1281BEC1 Protein-17.882-163.799207.721
41.7228-1.0843-0.31821.55660.18940.0768-0.0073-0.0134-0.0136-0.00240.0344-0.1813-0.0232-0.0195-0.02710.07660.01120.10270.0350.0080.175BEC2 Protein19.654-189.221193.343
52.3899-0.8663-0.85830.7490.51920.44460.09220.2028-0.18210.0264-0.08580.0445-0.0718-0.079-0.00640.13570.01390.10160.0489-0.00790.1158CEC1 Protein12.207-165.298182.903
62.1498-1.76030.01991.47830.00491.1149-0.0499-0.13310.0312-0.05020.1097-0.08590.0012-0.0711-0.05980.2103-0.0130.14110.015-0.01080.1018CEC2 Protein-28.18-142.087193.68
70.42190.3318-0.92130.9539-0.60072.06030.0046-0.07790.0407-0.08060.0945-0.0576-0.02970.1634-0.0990.06680.00410.0980.0943-0.01580.1633DEC1 Protein-6.148-155.457156.313
80.97420.8024-0.95862.2322-1.55271.5313-0.05550.02740.14460.04210.2157-0.22540.1744-0.1976-0.16020.1419-0.045-0.15930.05210.02530.2516DEC2 Protein-25.535-178.691193.434
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 100
2X-RAY DIFFRACTION1A1001 - 1003
3X-RAY DIFFRACTION2A101 - 215
4X-RAY DIFFRACTION2A1004
5X-RAY DIFFRACTION3B0 - 100
6X-RAY DIFFRACTION3B301 - 303
7X-RAY DIFFRACTION4B101 - 215
8X-RAY DIFFRACTION4B304
9X-RAY DIFFRACTION5C1 - 100
10X-RAY DIFFRACTION5C301 - 303
11X-RAY DIFFRACTION6C101 - 216
12X-RAY DIFFRACTION6C304
13X-RAY DIFFRACTION7D0 - 100
14X-RAY DIFFRACTION7D301 - 303
15X-RAY DIFFRACTION8D101 - 215
16X-RAY DIFFRACTION8D304

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