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- PDB-7rgf: Protocadherin gammaC4 EC1-4 crystal structure disrupted trans int... -

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Basic information

Entry
Database: PDB / ID: 7rgf
TitleProtocadherin gammaC4 EC1-4 crystal structure disrupted trans interface
ComponentsProtocadherin gamma C4
KeywordsCELL ADHESION / Cadherin / Cell-surface receptor / Neuronal self-avoidance
Function / homology
Function and homology information


homophilic cell adhesion via plasma membrane adhesion molecules / synapse organization / negative regulation of neuron apoptotic process / membrane => GO:0016020 / calcium ion binding / membrane / plasma membrane
Similarity search - Function
Cadherin, C-terminal catenin-binding domain / Cadherin C-terminal cytoplasmic tail, catenin-binding region / Cadherin, N-terminal / Cadherin-like / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / Protocadherin gamma C4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGoodman, K.M. / Mannepalli, S. / Honig, B. / Shapiro, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01MH114817 United States
CitationJournal: Elife / Year: 2022
Title: How clustered protocadherin binding specificity is tuned for neuronal self-/nonself-recognition.
Authors: Goodman, K.M. / Katsamba, P.S. / Rubinstein, R. / Ahlsen, G. / Bahna, F. / Mannepalli, S. / Dan, H. / Sampogna, R.V. / Shapiro, L. / Honig, B.
History
DepositionJul 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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: Protocadherin gamma C4
B: Protocadherin gamma C4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,92136
Polymers94,0142
Non-polymers4,90734
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-95 kcal/mol
Surface area46000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.944, 103.948, 200.592
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNVALVAL(chain 'A' and (resid 1 through 20 or resid 22...AA1 - 191 - 19
12ASPASPTHRTHR(chain 'A' and (resid 1 through 20 or resid 22...AA22 - 2722 - 27
13LEULEUSERSER(chain 'A' and (resid 1 through 20 or resid 22...AA30 - 3130 - 31
14ARGARGGLNGLN(chain 'A' and (resid 1 through 20 or resid 22...AA34 - 12134 - 121
15PHEPHELEULEU(chain 'A' and (resid 1 through 20 or resid 22...AA123 - 125123 - 125
16ALAALAGLUGLU(chain 'A' and (resid 1 through 20 or resid 22...AA128 - 326128 - 326
17GLYGLYILEILE(chain 'A' and (resid 1 through 20 or resid 22...AA328 - 394328 - 394
18VALVALSERSER(chain 'A' and (resid 1 through 20 or resid 22...AA396 - 417396 - 417
21GLNGLNVALVAL(chain 'B' and (resid 1 through 11 or (resid 12...BB1 - 191 - 19
22ASPASPTHRTHR(chain 'B' and (resid 1 through 11 or (resid 12...BB22 - 2722 - 27
23LEULEUSERSER(chain 'B' and (resid 1 through 11 or (resid 12...BB30 - 3130 - 31
24ARGARGGLNGLN(chain 'B' and (resid 1 through 11 or (resid 12...BB34 - 12134 - 121
25PHEPHELEULEU(chain 'B' and (resid 1 through 11 or (resid 12...BB123 - 125123 - 125
26ALAALAGLUGLU(chain 'B' and (resid 1 through 11 or (resid 12...BB128 - 326128 - 326
27GLYGLYILEILE(chain 'B' and (resid 1 through 11 or (resid 12...BB328 - 394328 - 394
28VALVALSERSER(chain 'B' and (resid 1 through 11 or (resid 12...BB396 - 417396 - 417

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protocadherin gamma C4 / Protocadherin gamma subfamily C / 4


Mass: 47006.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdhgc4 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q91XX0

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Sugars , 4 types, 8 molecules

#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1422.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-4-3-5/a4-b1_a6-h1_b4-c1_c3-d1_c6-g1_d2-e1_e4-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1260.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
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
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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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Non-polymers , 4 types, 151 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Formula: Ca
#8: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 293 K / Method: batch mode / Details: 1 M LiCl, 0.1 M Mes pH 6.0, and 10% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 42979 / % possible obs: 98.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 51.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.04 / Rrim(I) all: 0.073 / Net I/σ(I): 13.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4175 / CC1/2: 0.924 / Rpim(I) all: 0.342 / Rrim(I) all: 0.56 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JGZ

7jgz


Resolution: 2.4→38.16 Å / SU ML: 0.3231 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0313 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2405 2144 5.01 %
Rwork0.1956 40671 -
obs0.1977 42815 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.39 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6327 0 284 125 6736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036736
X-RAY DIFFRACTIONf_angle_d0.65339217
X-RAY DIFFRACTIONf_chiral_restr0.04321108
X-RAY DIFFRACTIONf_plane_restr0.00411210
X-RAY DIFFRACTIONf_dihedral_angle_d15.57563984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.37461450.31072430X-RAY DIFFRACTION89.66
2.46-2.520.34621640.28392583X-RAY DIFFRACTION97
2.52-2.590.35751440.28012700X-RAY DIFFRACTION99.06
2.59-2.660.32991310.27982686X-RAY DIFFRACTION99.12
2.66-2.750.31291660.25362687X-RAY DIFFRACTION99.55
2.75-2.850.31071380.26052680X-RAY DIFFRACTION99.16
2.85-2.960.32521300.24792710X-RAY DIFFRACTION98.85
2.96-3.090.29131410.23912727X-RAY DIFFRACTION99.38
3.09-3.260.2981430.23872729X-RAY DIFFRACTION99.24
3.26-3.460.27071390.22072748X-RAY DIFFRACTION99.83
3.46-3.730.22371300.20112754X-RAY DIFFRACTION99.83
3.73-4.10.25121360.18112740X-RAY DIFFRACTION99.45
4.1-4.70.17011470.15282783X-RAY DIFFRACTION99.29
4.7-5.910.19351410.15462810X-RAY DIFFRACTION99.29
5.91-38.160.19561490.15712904X-RAY DIFFRACTION97.98
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)
14.583854435820.418904296575-1.14660997813.630878939910.6711881444393.77080921405-0.005603398717250.23305522619-0.176708566961-0.07076047259020.204243446699-0.02847704204990.609679601749-0.111033660411-0.2037197519760.361372380476-0.0393875657949-0.0227528488240.414714546578-0.02588203101950.38476753209735.1871228536228.279553796101.625032439
23.81822980082-0.796539423761-1.775058267712.7495020342-0.5380722577333.107073244570.5190575131160.0799351079247-0.188169068096-0.675035267711-0.05532965873260.09694705889311.089489141320.0177537574338-0.4583785412071.013826020070.25427544011-0.0709059079370.8191782595680.04424836092280.483123026828-11.1845008113225.046060063-23.9067679603
33.287539168881.756949981793.827689669462.024961905251.742320666074.44274959670.1350567381190.202050085086-0.0954221945241-0.2182033879730.367233378162-0.0657448519537-0.1341397116390.74557744279-0.5333865030830.78909719038-0.1140149672960.02341413535010.870193176578-0.1161586566920.51744565803727.2230043122226.49065549558.4165443671
42.33315213827-0.0721737113906-1.113289614493.021328719451.32181181537.031738422220.209942655424-0.09995678692770.0436927615311-0.3048116643230.0210279005299-0.0692762680978-1.23668639739-0.344857375624-0.1965386647310.5782710087360.02322417362940.02298685004580.383792378936-0.05427593976170.39334632539814.926337791215.26051245110.1265234309
52.5276946155-0.1848783293830.3712114641192.63300355273-0.519282202062.251590407820.07784487237950.4241833982410.166238554789-0.02042089475590.2186525501020.260679652624-1.55021609948-0.960731286971-0.1465640282751.221366033670.3657439568470.2449627600910.8153335078420.1833976631790.5689468541979.34241281708217.212641342-38.4372788759
62.94796535973-0.868452181384.264534133192.49510784332-1.906475591349.544253258180.249528659183-0.0508449673249-0.1563140895950.1335627410520.07957447598550.0397897925353-0.1239031624830.212639641237-0.3124788728540.5424765527760.01400556866480.02092473979260.6223575036470.01327994833060.399240323228-3.27100916041226.40454138819.3342350716
71.314798294590.08675792811360.3494793379111.344401717010.9372956871826.642416529070.0277366461330.206051081334-0.0394039934025-0.2213535662790.237483269116-0.03008178656120.02542806157610.494182991498-0.2399283546430.5320112476690.00782215271566-0.06136474506030.515033342990.008826668229560.360868271729.12308170627216.17197469367.7832995689
83.699380931820.5110109720311.780686510892.91210295608-0.3308144986177.286893625130.100244177336-0.5988181672540.04778203724060.410676518051-0.033757022588-0.1107994184190.00772827152221-0.0929162071606-0.09008574670740.4211514929370.04554995968220.06268339137180.386895182597-0.004081728491740.35110228933916.8259585061219.049223308116.166832241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 97)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 97)
3X-RAY DIFFRACTION3(chain 'A' and resid 98 through 206)
4X-RAY DIFFRACTION4(chain 'A' and resid 207 through 314)
5X-RAY DIFFRACTION5(chain 'A' and resid 315 through 418)
6X-RAY DIFFRACTION6(chain 'B' and resid 98 through 206)
7X-RAY DIFFRACTION7(chain 'B' and resid 207 through 314)
8X-RAY DIFFRACTION8(chain 'B' and resid 315 through 418)

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