[English] 日本語
Yorodumi
- PDB-7rgf: Protocadherin gammaC4 EC1-4 crystal structure disrupted trans int... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / Cadherin-like ...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 / Cadherin-like / Cadherins domain profile. / 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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


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


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

-
Non-polymers , 4 types, 151 molecules

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


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


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


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more