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- PDB-8ah4: Crystal Structure of the third PDZ domain of PSD-95 protein in th... -

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Basic information

Entry
Database: PDB / ID: 8ah4
TitleCrystal Structure of the third PDZ domain of PSD-95 protein in the space group P3112 at pH 4.0
ComponentscDNA FLJ50577, highly similar to Discs large homolog 4
KeywordsPROTEIN BINDING / PDZ domain
Function / homology
Function and homology information


neuromuscular junction / kinase binding / chemical synaptic transmission / neuron projection
Similarity search - Function
PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. ...PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / cDNA FLJ50577, highly similar to Discs large homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 Å
Model detailspH 4.0 P3112 polymorph
AuthorsCamara-Artigas, A. / Salinas Garcia, M.C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Other governmentUAL-FEDER-UAL18-BIO-B005-B Spain
CitationJournal: Crystals / Year: 2023
Title: pH-Driven Polymorphic Behaviour of the Third PDZ Domain of PSD95: The Role of Electrostatic Interactions
Authors: Salinas-Garcia, M.C. / Plaza-Garrido, M. / Gavira, J.A. / Murciano-Calles, J. / Andujar-Sanchez, M. / Ortiz-Salmeron, E. / Martinez, J.C. / Camara-Artigas, A.
History
DepositionJul 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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: cDNA FLJ50577, highly similar to Discs large homolog 4
B: cDNA FLJ50577, highly similar to Discs large homolog 4
C: cDNA FLJ50577, highly similar to Discs large homolog 4
D: cDNA FLJ50577, highly similar to Discs large homolog 4
E: cDNA FLJ50577, highly similar to Discs large homolog 4
F: cDNA FLJ50577, highly similar to Discs large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,24512
Polymers66,8916
Non-polymers3546
Water9,260514
1
A: cDNA FLJ50577, highly similar to Discs large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2673
Polymers11,1481
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cDNA FLJ50577, highly similar to Discs large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2082
Polymers11,1481
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: cDNA FLJ50577, highly similar to Discs large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2082
Polymers11,1481
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: cDNA FLJ50577, highly similar to Discs large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2082
Polymers11,1481
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: cDNA FLJ50577, highly similar to Discs large homolog 4


Theoretical massNumber of molelcules
Total (without water)11,1481
Polymers11,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: cDNA FLJ50577, highly similar to Discs large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2082
Polymers11,1481
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.698, 61.698, 228.702
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11B-668-

HOH

21D-665-

HOH

31E-535-

HOH

41E-579-

HOH

51F-663-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 309 through 310 and (name N...
21(chain B and (resid 309 through 311 or resid 313...
31(chain C and ((resid 309 through 310 and (name N...
41(chain D and (resid 309 through 311 or resid 313...
51(chain E and (resid 309 through 311 or resid 313...
61(chain F and (resid 309 through 311 or resid 313...

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
11ARGARGGLUGLU(chain A and ((resid 309 through 310 and (name N...AA309 - 31010 - 11
12PROPROGLUGLU(chain A and ((resid 309 through 310 and (name N...AA308 - 4019 - 102
13PROPROGLUGLU(chain A and ((resid 309 through 310 and (name N...AA308 - 4019 - 102
14PROPROGLUGLU(chain A and ((resid 309 through 310 and (name N...AA308 - 4019 - 102
15PROPROGLUGLU(chain A and ((resid 309 through 310 and (name N...AA308 - 4019 - 102
21ARGARGPROPRO(chain B and (resid 309 through 311 or resid 313...BB309 - 31110 - 12
22ARGARGGLYGLY(chain B and (resid 309 through 311 or resid 313...BB313 - 31914 - 20
23SERSERTHRTHR(chain B and (resid 309 through 311 or resid 313...BB320 - 32121 - 22
24ILEILEACTACT(chain B and (resid 309 through 311 or resid 313...BB - I307 - 5018
25ILEILEACTACT(chain B and (resid 309 through 311 or resid 313...BB - I307 - 5018
26ILEILEACTACT(chain B and (resid 309 through 311 or resid 313...BB - I307 - 5018
27ILEILEACTACT(chain B and (resid 309 through 311 or resid 313...BB - I307 - 5018
31ARGARGGLUGLU(chain C and ((resid 309 through 310 and (name N...CC309 - 31010 - 11
32PROPROGLUGLU(chain C and ((resid 309 through 310 and (name N...CC308 - 4019 - 102
33PROPROGLUGLU(chain C and ((resid 309 through 310 and (name N...CC308 - 4019 - 102
34PROPROGLUGLU(chain C and ((resid 309 through 310 and (name N...CC308 - 4019 - 102
35PROPROGLUGLU(chain C and ((resid 309 through 310 and (name N...CC308 - 4019 - 102
41ARGARGPROPRO(chain D and (resid 309 through 311 or resid 313...DD309 - 31110 - 12
42ARGARGGLYGLY(chain D and (resid 309 through 311 or resid 313...DD313 - 33014 - 31
43ASPASPGLYGLY(chain D and (resid 309 through 311 or resid 313...DD332 - 33333 - 34
44GLYGLYLEULEU(chain D and (resid 309 through 311 or resid 313...DD335 - 35336 - 54
45ARGARGLYSLYS(chain D and (resid 309 through 311 or resid 313...DD354 - 35555 - 56
46ARGARGPHEPHE(chain D and (resid 309 through 311 or resid 313...DD309 - 40010 - 101
47ARGARGPHEPHE(chain D and (resid 309 through 311 or resid 313...DD309 - 40010 - 101
48ARGARGPHEPHE(chain D and (resid 309 through 311 or resid 313...DD309 - 40010 - 101
49ARGARGPHEPHE(chain D and (resid 309 through 311 or resid 313...DD309 - 40010 - 101
51ARGARGPROPRO(chain E and (resid 309 through 311 or resid 313...EE309 - 31110 - 12
52ARGARGGLYGLY(chain E and (resid 309 through 311 or resid 313...EE313 - 31914 - 20
53SERSERTHRTHR(chain E and (resid 309 through 311 or resid 313...EE320 - 32121 - 22
54ARGARGALAALA(chain E and (resid 309 through 311 or resid 313...EE309 - 40210 - 103
55ARGARGALAALA(chain E and (resid 309 through 311 or resid 313...EE309 - 40210 - 103
56ARGARGALAALA(chain E and (resid 309 through 311 or resid 313...EE309 - 40210 - 103
57ARGARGALAALA(chain E and (resid 309 through 311 or resid 313...EE309 - 40210 - 103
61ARGARGPROPRO(chain F and (resid 309 through 311 or resid 313...FF309 - 31110 - 12
62ARGARGGLYGLY(chain F and (resid 309 through 311 or resid 313...FF313 - 31914 - 20
63SERSERTHRTHR(chain F and (resid 309 through 311 or resid 313...FF320 - 32121 - 22
64PROPROLYSLYS(chain F and (resid 309 through 311 or resid 313...FF308 - 4039 - 104
65PROPROLYSLYS(chain F and (resid 309 through 311 or resid 313...FF308 - 4039 - 104
66PROPROLYSLYS(chain F and (resid 309 through 311 or resid 313...FF308 - 4039 - 104
67PROPROLYSLYS(chain F and (resid 309 through 311 or resid 313...FF308 - 4039 - 104

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Components

#1: Protein
cDNA FLJ50577, highly similar to Discs large homolog 4


Mass: 11148.488 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7Z4H2
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O
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: 1.88 Å3/Da / Density % sol: 34.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 30% PEG4K, 0.2M AMSO4, 0.1M AcONa

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.478→52.031 Å / Num. obs: 59113 / % possible obs: 93.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 16.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.1
Reflection shellResolution: 1.478→1.635 Å / Rmerge(I) obs: 0.692 / Num. unique obs: 2957 / CC1/2: 0.722

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.2refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QJI

6qji


Resolution: 1.48→48.41 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 2882 4.89 %
Rwork0.1949 56098 -
obs0.1966 58980 70.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.59 Å2 / Biso mean: 24.411 Å2 / Biso min: 9.02 Å2
Refinement stepCycle: final / Resolution: 1.48→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 42 516 4698
Biso mean--38.28 30.46 -
Num. residues----565
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2179X-RAY DIFFRACTION8.376TORSIONAL
12B2179X-RAY DIFFRACTION8.376TORSIONAL
13C2179X-RAY DIFFRACTION8.376TORSIONAL
14D2179X-RAY DIFFRACTION8.376TORSIONAL
15E2179X-RAY DIFFRACTION8.376TORSIONAL
16F2179X-RAY DIFFRACTION8.376TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.48-1.50.495930.36491281313
1.5-1.530.430360.29992372436
1.53-1.560.3409280.314242645412
1.56-1.590.4079370.293261665316
1.59-1.620.3122420.290787591723
1.62-1.650.3212780.27641128120631
1.65-1.690.3361740.25841548162241
1.69-1.730.27961420.2662675281771
1.73-1.780.27061830.2573442362591
1.78-1.830.27961760.24113739391599
1.83-1.890.27471920.225937683960100
1.89-1.960.2471710.213738253996100
1.96-2.040.2191850.19837973982100
2.04-2.130.23752070.18673788399599
2.13-2.240.22811990.18163743394299
2.24-2.380.20862140.183753396798
2.39-2.570.23121740.19143751392598
2.57-2.830.24111890.18843656384596
2.83-3.240.19961630.17413525368891
3.24-4.080.21062150.159438394054100
4.08-48.410.21942040.20973839404397

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