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- PDB-5szl: Protocadherin gamma A1 extracellular cadherin domains 1-4 -

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Basic information

Entry
Database: PDB / ID: 5szl
TitleProtocadherin gamma A1 extracellular cadherin domains 1-4
ComponentsPROTOCADHERIN GAMMA A1 EXTRACELLULAR CADHERIN DOMAINS 1-4, Protein Pcdhga1
KeywordsCELL ADHESION
Function / homology
Function and homology information


homophilic cell-cell adhesion / cell adhesion molecule binding / cell adhesion / calcium ion binding / membrane / plasma membrane
Similarity search - Function
Cadherin, C-terminal catenin-binding domain / Cadherin C-terminal cytoplasmic tail, catenin-binding region / Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / : / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. ...Cadherin, C-terminal catenin-binding domain / Cadherin C-terminal cytoplasmic tail, catenin-binding region / Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / : / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / Protocadherin gamma subfamily A, 1 / Protocadherin gamma A1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsGoodman, K.M. / Bahna, F. / Mannepalli, S. / Honig, B. / Shapiro, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM107571 United States
CitationJournal: Elife / Year: 2016
Title: gamma-Protocadherin structural diversity and functional implications.
Authors: Goodman, K.M. / Rubinstein, R. / Thu, C.A. / Mannepalli, S. / Bahna, F. / Ahlsen, G. / Rittenhouse, C. / Maniatis, T. / Honig, B. / Shapiro, L.
History
DepositionAug 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 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 GAMMA A1 EXTRACELLULAR CADHERIN DOMAINS 1-4, Protein Pcdhga1
B: PROTOCADHERIN GAMMA A1 EXTRACELLULAR CADHERIN DOMAINS 1-4, Protein Pcdhga1
C: PROTOCADHERIN GAMMA A1 EXTRACELLULAR CADHERIN DOMAINS 1-4, Protein Pcdhga1
D: PROTOCADHERIN GAMMA A1 EXTRACELLULAR CADHERIN DOMAINS 1-4, Protein Pcdhga1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,05756
Polymers189,3234
Non-polymers5,73452
Water00
1
A: PROTOCADHERIN GAMMA A1 EXTRACELLULAR CADHERIN DOMAINS 1-4, Protein Pcdhga1
B: PROTOCADHERIN GAMMA A1 EXTRACELLULAR CADHERIN DOMAINS 1-4, Protein Pcdhga1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,35428
Polymers94,6612
Non-polymers2,69226
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-64 kcal/mol
Surface area44440 Å2
MethodPISA
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C: PROTOCADHERIN GAMMA A1 EXTRACELLULAR CADHERIN DOMAINS 1-4, Protein Pcdhga1
D: PROTOCADHERIN GAMMA A1 EXTRACELLULAR CADHERIN DOMAINS 1-4, Protein Pcdhga1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,70328
Polymers94,6612
Non-polymers3,04226
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-70 kcal/mol
Surface area45630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.867, 107.867, 463.081
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Non-polymers , 2 types, 40 molecules ABCD

#1: Protein
PROTOCADHERIN GAMMA A1 EXTRACELLULAR CADHERIN DOMAINS 1-4, Protein Pcdhga1


Mass: 47330.723 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdhga1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: A0A0A6YW27, UniProt: Q91XZ0*PLUS
#6: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Ca

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Sugars , 5 types, 16 molecules

#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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 8
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
#7: 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.: 5
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

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Details

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: 4.11 Å3/Da / Density % sol: 70.06 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 7
Details: 8% (w/v) PEG8000, 16% ethylene glycol, 20% Morpheus Amino Acids (Molecular Dimensions), 0.1 M Morpheus Buffer System 2 (Hepes/MOPS buffer; Molecular Dimensions) pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 4.2→40 Å / Num. obs: 23885 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 133.85 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.379 / Net I/σ(I): 3.1
Reflection shellResolution: 4.2→4.54 Å / Redundancy: 3.6 % / Rmerge(I) obs: 2.646 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.318 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZI9

4zi9


Resolution: 4.2→39.96 Å / SU ML: 0.81 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.07
RfactorNum. reflection% reflection
Rfree0.3136 1182 5 %
Rwork0.2866 --
obs0.2879 23652 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.2→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12195 0 310 0 12505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412722
X-RAY DIFFRACTIONf_angle_d0.82217450
X-RAY DIFFRACTIONf_dihedral_angle_d11.6697767
X-RAY DIFFRACTIONf_chiral_restr0.0542112
X-RAY DIFFRACTIONf_plane_restr0.0052332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2-4.39090.41611710.36852612X-RAY DIFFRACTION96
4.3909-4.62210.40021620.36562726X-RAY DIFFRACTION99
4.6221-4.91120.40171420.34432807X-RAY DIFFRACTION99
4.9112-5.28960.33671430.30782751X-RAY DIFFRACTION100
5.2896-5.82050.34471480.31092814X-RAY DIFFRACTION100
5.8205-6.65940.33841350.30922846X-RAY DIFFRACTION100
6.6594-8.37740.32071480.29132872X-RAY DIFFRACTION100
8.3774-39.96180.22641330.22093042X-RAY DIFFRACTION99
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)
10.0375-0.02910.0060.0105-0.03170.01770.517-0.21320.6457-0.05140.3854-0.42140.01110.125602.72410.0662-0.52881.6569-0.37092.356969.990773.7472110.9653
2-0.02050.0791-0.0154-0.0006-0.10820.03310.21780.2411-0.2533-0.146-0.02420.3502-0.07460.030602.191-0.118-0.51562.232-0.30512.2804-19.8850.830135.2583
30.05520.0925-0.03590.0275-0.16480.06490.11650.6798-0.1120.1021-0.1339-0.1313-0.244-0.388101.58740.2905-0.10832.08990.15581.237910.484848.4909-8.8076
4-0.01870.09130.0563-0.0482-0.03910.0532-1.07650.31130.22430.06630.1978-0.25430.0691-0.2472-02.96820.0460.13151.5728-0.33591.33864.343954.1856130.1291
50.1737-0.0233-0.02520.1962-0.26640.1793-0.19550.1479-0.40540.11810.1302-0.3646-0.23240.1092-01.37840.2796-0.13040.9731-0.21761.281444.066553.7781.8585
60.3442-0.0992-0.16230.2781-0.14950.1515-0.42220.1688-0.0460.67130.29890.08030.3776-0.2309-01.50650.011-0.1011.2959-0.31811.25286.465121.880963.2482
70.1628-0.1919-0.22890.3655-0.1070.0935-0.33630.0430.275-0.2480.29860.2357-0.0122-0.0438-01.4540.2268-0.09140.9619-0.04711.340616.106948.15635.145
80.3721-0.0611-0.06360.22040.02290.07750.4589-0.13610.72080.4572-0.04460.2351.1159-0.107501.58270.104-0.07111.3191-0.25831.28985.025546.194886.6191
90.21460.1008-0.1034-0.0982-0.03280.13060.76560.13640.016-0.3125-0.5624-0.24640.0920.552201.32330.7222-0.18340.9457-0.08720.861420.689524.705746.621
10-0.0221-0.10370.0375-0.17960.12230.0467-0.0023-0.0807-0.2162-0.19420.77890.2053-0.0044-0.21050-1.08484.16060.4359-4.4486-1.74930.946442.607837.710796.5637
110.01340.0075-0.0511-0.02490.09690.0559-0.30750.7131-0.1906-0.05530.141-0.16550.5435-0.0345-01.20641.1446-0.2540.04570.16221.023220.331462.080484.0466
120.21660.06370.1290.2727-0.05230.0415-0.13-0.67460.1997-0.9443-0.8837-0.3379-0.0271-0.0017-01.71450.508-0.23261.1093-0.23551.3794-6.040848.436736.6976
13-0.04720.07560.24510.1048-0.2420.09430.21260.4910.5741-0.02250.29260.2658-0.8186-0.5468-01.87220.0124-0.35491.6005-0.34031.699-6.05735.63413.4279
140.1061-0.1533-0.21160.04440.08850.09860.56320.7247-0.760.1981-0.15951.1801-0.5575-0.065303.05880.1708-0.68251.728-0.29822.768469.382956.208128.0153
150.4411-0.1266-0.06980.0056-0.06890.02970.03860.26770.1107-0.35380.1265-0.0788-0.88441.030201.52220.2445-0.11751.14760.22370.979734.963370.1768129.8166
16-0.30310.11840.0062-0.04030.0766-0.013-0.6357-0.5462-0.28330.07080.09320.2391-0.1597-0.3201-00.0564-0.4051-0.97670.7109-2.4015-5.287-25.55640.0443-7.8167
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:98 )A2 - 98
2X-RAY DIFFRACTION2( CHAIN B AND RESID 2:98 )B2 - 98
3X-RAY DIFFRACTION3( CHAIN C AND RESID 2:98 )C2 - 98
4X-RAY DIFFRACTION4( CHAIN D AND RESID 2:98 )D2 - 98
5X-RAY DIFFRACTION5( CHAIN A AND RESID 99:207 )A99 - 207
6X-RAY DIFFRACTION6( CHAIN B AND RESID 99:207 )B99 - 207
7X-RAY DIFFRACTION7( CHAIN C AND RESID 99:207 )C99 - 207
8X-RAY DIFFRACTION8( CHAIN D AND RESID 99:207 )D99 - 207
9X-RAY DIFFRACTION9( CHAIN A AND RESID 208:312 )A208 - 312
10X-RAY DIFFRACTION10( CHAIN B AND RESID 208:312 )B208 - 312
11X-RAY DIFFRACTION11( CHAIN C AND RESID 208:312 )C208 - 312
12X-RAY DIFFRACTION12( CHAIN D AND RESID 208:312 )D208 - 312
13X-RAY DIFFRACTION13( CHAIN A AND RESID 313:414 )A313 - 414
14X-RAY DIFFRACTION14( CHAIN B AND RESID 313:413 )B313 - 413
15X-RAY DIFFRACTION15( CHAIN C AND RESID 313:419 )C313 - 419
16X-RAY DIFFRACTION16( CHAIN D AND RESID 313:417 )D313 - 417

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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