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- PDB-6mga: Crystal Structure of Human Protocadherin-1 EC1-4 with glycosylation -

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Basic information

Entry
Database: PDB / ID: 6mga
TitleCrystal Structure of Human Protocadherin-1 EC1-4 with glycosylation
ComponentsProtocadherin-1
KeywordsCELL ADHESION / cadherins / adhesion / calcium-binding protein / asthma
Function / homology
Function and homology information


homophilic cell adhesion via plasma membrane adhesion molecules / cell junction / cell-cell junction / nervous system development / cell-cell signaling / cell adhesion / intracellular membrane-bounded organelle / calcium ion binding / nucleolus / nucleoplasm / plasma membrane
Similarity search - Function
Protocadherin / Protocadherin / Cadherin, N-terminal / Cadherin-like / : / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain ...Protocadherin / Protocadherin / Cadherin, N-terminal / Cadherin-like / : / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Protocadherin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsModak, D. / Sotomayor, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateAlfred P. Sloan FR-2015-65794 United States
CitationJournal: Commun Biol / Year: 2019
Title: Identification of an adhesive interface for the non-clustered delta 1 protocadherin-1 involved in respiratory diseases.
Authors: Modak, D. / Sotomayor, M.
History
DepositionSep 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protocadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,81412
Polymers50,0521
Non-polymers76211
Water00
1
A: Protocadherin-1
hetero molecules

A: Protocadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,62824
Polymers100,1042
Non-polymers1,52422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
2
A: Protocadherin-1
hetero molecules

A: Protocadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,62824
Polymers100,1042
Non-polymers1,52422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area4200 Å2
ΔGint-86 kcal/mol
Surface area47060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.227, 147.227, 149.366
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Protocadherin-1 / Cadherin-like protein 1 / Protocadherin-42 / PC42


Mass: 50052.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCDH1 / Cell line (production host): Expi 293F / Production host: Homo sapiens (human) / References: UniProt: Q08174
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
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: 4.7 Å3/Da / Density % sol: 73.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Magnesium Chloride, 0.05 M Tris HCl pH 8.5, 30% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 17231 / % possible obs: 100 % / Redundancy: 36.4 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.013 / Rrim(I) all: 0.079 / Net I/σ(I): 58
Reflection shellResolution: 3.15→3.2 Å / Redundancy: 28.2 % / Rmerge(I) obs: 1.762 / Mean I/σ(I) obs: 2.5 / Num. unique all: 823 / Rpim(I) all: 0.321 / Rrim(I) all: 1.792 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BX7

6bx7


Resolution: 3.15→48.53 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / SU B: 38.954 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R: 0.722 / ESU R Free: 0.381 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26342 820 4.8 %RANDOM
Rwork0.21481 ---
obs0.21715 16280 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 146.584 Å2
Baniso -1Baniso -2Baniso -3
1-2.8 Å21.4 Å20 Å2
2--2.8 Å2-0 Å2
3----9.07 Å2
Refinement stepCycle: 1 / Resolution: 3.15→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 34 0 3318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0143363
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172991
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.6734583
X-RAY DIFFRACTIONr_angle_other_deg0.8681.6427058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2995427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66824.066182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.33415557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7391521
X-RAY DIFFRACTIONr_chiral_restr0.0660.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023810
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02524
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_it4.83210.8971714
X-RAY DIFFRACTIONr_mcbond_other4.83310.8951713
X-RAY DIFFRACTIONr_mcangle_it7.49616.3462139
X-RAY DIFFRACTIONr_mcangle_other7.49516.3492140
X-RAY DIFFRACTIONr_scbond_it5.10311.3371648
X-RAY DIFFRACTIONr_scbond_other5.10211.3381648
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.95416.8612445
X-RAY DIFFRACTIONr_long_range_B_refined12.61513127
X-RAY DIFFRACTIONr_long_range_B_other12.60713124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.141→3.223 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 51 -
Rwork0.333 1150 -
obs--97.17 %
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)Origin x (Å)Origin y (Å)Origin z (Å)
12.5333-1.4767-2.25065.49594.17514.29170.1933-0.59680.60560.5406-0.06080.227-0.3776-0.0699-0.13250.9360.1421-0.02850.6251-0.12670.464358.005220.613761.0567
20.310.15490.82350.15481.09058.3154-0.0462-0.0396-0.1010.03960.0227-0.03640.25910.29960.02350.34720.0042-0.04830.03880.00860.259265.5816-0.806823.0245
32.71582.84124.21163.56954.6537.91130.0221-0.01510.0147-0.0958-0.16460.4743-0.0085-0.46240.14240.2535-0.048-0.00930.1736-0.12090.385648.6049-18.4172-20.2252
40.8742-0.09820.06930.7028-0.57398.38290.08790.49550.1808-0.5118-0.1902-0.11320.08150.09360.10230.66720.0117-0.04730.5361-0.08390.559439.9762-37.2493-62.9427
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 106
2X-RAY DIFFRACTION1A503 - 504
3X-RAY DIFFRACTION2A107 - 218
4X-RAY DIFFRACTION2A505 - 507
5X-RAY DIFFRACTION3A219 - 325
6X-RAY DIFFRACTION3A508 - 510
7X-RAY DIFFRACTION4A326 - 439
8X-RAY DIFFRACTION4A511

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