[English] 日本語
Yorodumi
- PDB-4wj7: CCM2 PTB domain in complex with KRIT1 NPxY/F3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wj7
TitleCCM2 PTB domain in complex with KRIT1 NPxY/F3
Components
  • KRIT1 NPxY/F3
  • Malcavernin
KeywordsPROTEIN BINDING / Complex / PTB domain / NPxY motif
Function / homology
Function and homology information


endothelial cell development / venous blood vessel morphogenesis / blood vessel endothelial cell differentiation / pericardium development / endothelium development / endothelial tube morphogenesis / cell-cell junction organization / inner ear development / vasculogenesis / regulation of angiogenesis ...endothelial cell development / venous blood vessel morphogenesis / blood vessel endothelial cell differentiation / pericardium development / endothelium development / endothelial tube morphogenesis / cell-cell junction organization / inner ear development / vasculogenesis / regulation of angiogenesis / stress-activated MAPK cascade / integrin-mediated signaling pathway / multicellular organism growth / heart development / in utero embryonic development / protein-containing complex / mitochondrion / cytoplasm
Similarity search - Function
Cerebral cavernous malformations 2 / Cerebral cavernous malformations 2, harmonin-homology domain / Cerebral cavernous malformation protein, harmonin-homology / Phosphotyrosine interaction domain (PID) profile. / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Cerebral cavernous malformations 2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.753 Å
AuthorsFisher, O.S. / Liu, W. / Zhang, R. / Stiegler, A.L. / Boggon, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS085078 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for the Disruption of the Cerebral Cavernous Malformations 2 (CCM2) Interaction with Krev Interaction Trapped 1 (KRIT1) by Disease-associated Mutations.
Authors: Fisher, O.S. / Liu, W. / Zhang, R. / Stiegler, A.L. / Ghedia, S. / Weber, J.L. / Boggon, T.J.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.pdbx_ordinal / _struct_keywords.text
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Malcavernin
B: Malcavernin
C: Malcavernin
D: Malcavernin
W: KRIT1 NPxY/F3
X: KRIT1 NPxY/F3
Y: KRIT1 NPxY/F3
Z: KRIT1 NPxY/F3


Theoretical massNumber of molelcules
Total (without water)83,7798
Polymers83,7798
Non-polymers00
Water18010
1
A: Malcavernin
W: KRIT1 NPxY/F3


Theoretical massNumber of molelcules
Total (without water)20,9452
Polymers20,9452
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-10 kcal/mol
Surface area7880 Å2
MethodPISA
2
B: Malcavernin
X: KRIT1 NPxY/F3


Theoretical massNumber of molelcules
Total (without water)20,9452
Polymers20,9452
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-11 kcal/mol
Surface area8040 Å2
MethodPISA
3
C: Malcavernin
Y: KRIT1 NPxY/F3


Theoretical massNumber of molelcules
Total (without water)20,9452
Polymers20,9452
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-8 kcal/mol
Surface area7710 Å2
MethodPISA
4
D: Malcavernin
Z: KRIT1 NPxY/F3


Theoretical massNumber of molelcules
Total (without water)20,9452
Polymers20,9452
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-8 kcal/mol
Surface area7320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.938, 110.938, 315.255
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein
Malcavernin / Cerebral cavernous malformations 2 protein


Mass: 19523.039 Da / Num. of mol.: 4 / Fragment: PTB domain (UNP residues 51-228)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCM2, C7orf22, PP10187 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9BSQ5
#2: Protein/peptide
KRIT1 NPxY/F3


Mass: 1421.660 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% (w/v) PEG 6000, 0.1M HEPES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 30768 / % possible obs: 100 % / Redundancy: 17.9 % / Biso Wilson estimate: 93.7 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.07 / Net I/σ(I): 23
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 19 % / Mean I/σ(I) obs: 1.21 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC

4jif

3so6

3g9w

3hqc

3dxe

2ej8

2v76

1j0w

1wvh

2cy4

2dyq

1qqg

1x11

1aqc


Resolution: 2.753→29.669 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 1809 6.51 %Random
Rwork0.2198 25967 --
obs0.2218 27776 90.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 244.97 Å2 / Biso mean: 102.7045 Å2 / Biso min: 45.2 Å2
Refinement stepCycle: final / Resolution: 2.753→29.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4418 0 0 10 4428
Biso mean---69.16 -
Num. residues----566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044496
X-RAY DIFFRACTIONf_angle_d0.8686110
X-RAY DIFFRACTIONf_chiral_restr0.046731
X-RAY DIFFRACTIONf_plane_restr0.003772
X-RAY DIFFRACTIONf_dihedral_angle_d12.6921617
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.753-2.82690.44511060.36061424153066
2.8269-2.91010.35661010.34731552165371
2.9101-3.00390.36881110.34711651176277
3.0039-3.11120.37041210.31591729185081
3.1112-3.23560.31851440.28121983212792
3.2356-3.38260.27181460.25012083222996
3.3826-3.56070.25281520.22792171232399
3.5607-3.78340.25031480.22052156230499
3.7834-4.07480.2511500.20512132228296
4.0748-4.48360.20471500.16612166231698
4.4836-5.12950.181520.16132224237699
5.1295-6.45170.25911590.23122772436100
6.4517-29.67090.24011690.21582419258899
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)
13.09231.25062.75336.02550.30943.75380.4224-0.0169-0.2614-0.32630.1301-0.037-0.06970.2918-0.41610.62090.09280.09080.8026-0.09510.443831.625663.1281178.856
24.7571.35761.6338.69121.9376.47470.0852-0.80430.6590.4704-0.1899-0.338-1.05490.49150.14250.8506-0.04680.06170.7624-0.17090.555932.459375.3627190.798
39.16012.52842.00187.57334.20016.81460.62340.61.26060.0678-0.4233-0.894-1.4742-0.04480.13541.1511-0.00280.20960.87160.06990.62230.143373.5944172.9655
47.95272.16290.49493.26742.85696.947-0.97813.07970.9231-2.27260.5612-0.0075-0.6339-0.6319-0.21680.9416-0.05930.21261.1611-0.20180.429935.039867.9983169.4008
53.86660.773-0.53544.9123-1.99435.8703-0.0812-0.4666-0.00420.1461-0.04580.1397-0.29220.29390.01630.4957-0.0140.05330.7319-0.21490.367931.093465.0053182.0305
67.57080.118-0.84814.97030.17865.5788-0.2141-0.4395-0.4018-0.132-0.0473-0.12160.3139-0.37530.290.5542-0.03960.1060.7437-0.1150.392129.374560.6244180.1096
76.59833.40271.54558.88484.61013.27070.07820.853-0.1189-1.3322-0.3692-0.2747-0.2424-0.5340.02360.80020.14740.11910.93160.0740.430148.158758.8475147.0628
85.52520.0146-2.41658.15520.78677.84720.1972-0.61580.59120.2521-0.00020.2172-0.9449-0.0868-0.05790.5328-0.08440.14880.7827-0.02540.488748.796163.1208160.1507
95.6688-1.46562.23052.9427-2.33191.9595-0.69312.34780.5368-0.7372-0.0540.9945-2.5814-1.03810.77471.49540.0720.03781.23110.14020.615750.39164.7634143.0079
106.4065-1.4417-1.62334.9080.68455.65510.1966-0.17020.043-0.1403-0.31650.00490.00880.2620.17140.488-0.01880.13670.7986-0.03330.378450.373854.7718154.6196
114.98910.11261.82122.1803-1.35376.2797-0.28930.52990.2764-0.76660.2586-0.1442-0.57740.39270.24390.82620.0217-0.03840.91220.12650.665316.08274.0318147.5862
120.685-0.1020.45231.2874-0.05890.4980.2393-0.6477-0.83610.57970.27540.9394-0.5784-1.3846-0.62021.0056-0.164-0.08931.0916-0.00150.7185.620761.3654160.3661
132.8938-1.53221.66119.5506-1.69066.48350.44830.295-0.1972-1.1615-0.6865-0.00590.1390.70990.00370.67420.0745-0.04290.90890.01240.494416.465260.4304149.216
146.9407-3.3085-1.92965.18240.830.5337-0.34690.5064-0.1704-0.6662-0.56220.1092-1.693-1.18681.04121.29090.2449-0.10780.7430.10180.589110.187177.877146.6882
156.0364-6.4963-5.89477.01076.32035.75091.96452.69490.3009-2.0857-0.5175-0.8196-1.46840.00190.68371.5421-0.0105-0.01951.50910.40710.990517.202674.8149136.1138
167.28550.52120.09424.8657-3.13755.36630.4961-0.15060.5740.2275-0.4159-0.012-0.9067-0.3351-0.07610.68870.1245-0.12930.7173-0.08120.5879.973571.7336153.4695
172.32813.0966-1.62539.10040.53168.05040.3453-0.3759-0.45310.0722-0.2543-0.1243-0.3054-0.28450.21650.68970.1315-0.0360.67390.0790.397412.221164.5958155.4741
188.2997-5.80131.2546.833-0.40617.3169-0.0018-0.05361.3340.612-0.1592-1.2099-1.73740.0927-0.0310.9204-0.1264-0.04640.5661-0.0260.622216.42174.4726157.0206
192.1032-1.10310.05285.25393.0646.0025-1.0928-1.8016-0.97590.30230.967-0.2880.40230.40810.1041.6030.5532-0.07511.21720.18811.154526.676150.7119132.3023
206.7392-2.2501-4.99983.63210.0989.3771-0.18430.7109-0.70960.896-0.10221.85260.5839-1.80770.19571.67660.1139-0.061.16220.16141.029110.908753.6001124.0002
213.0954-3.09520.39354.45372.64726.588-0.109-1.5214-0.01971.36850.07590.7944-0.4502-1.6699-0.75331.62930.18220.16681.22290.05140.887119.752562.7836132.4585
226.8825-0.4134-3.21753.84690.57354.1952-0.6181-1.8733-0.6527-0.3330.3-0.03131.52072.1340.04452.26030.5874-0.29681.870.29321.431129.109348.4859137.3298
234.6287-0.96090.00927.8374-2.15074.38740.3802-0.1366-0.8092-0.0291-0.1809-0.15681.71750.6691-0.32861.79870.49450.02441.05280.10741.083322.854446.5772126.4942
249.7468-2.72222.05262.44520.46167.74791.09951.9741-0.5115-0.2182-1.10640.1084-0.2913-0.3385-0.07880.6211-0.0170.14950.53180.00480.403929.4255.02185.4908
255.1171-6.0408-4.53248.15595.05634.36730.07820.9435-0.8001-0.0256-0.30430.25050.3435-0.29650.0620.5650.09690.08370.72190.18060.429654.46347.7003158.3362
266.57222.27293.11645.27781.79089.1420.8939-0.20872.1657-0.0224-1.196-0.5119-1.97950.52490.73971.0505-0.19990.16230.98450.01040.48339.544972.603163.5324
272.19772.7342-0.26847.6641-1.01795.53710.16460.2005-3.87210.1037-1.7821-1.68691.60730.97450.40521.98630.0718-0.1110.905-0.15271.485718.313139.4499121.1728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 55 through 84 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 106 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 115 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 129 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 157 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 158 through 221 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 60 through 73 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 74 through 118 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 119 through 129 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 130 through 221 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 61 through 73 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 74 through 84 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 85 through 115 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 116 through 124 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 125 through 129 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 130 through 146 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 147 through 193 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 194 through 220 )C0
19X-RAY DIFFRACTION19chain 'D' and (resid 63 through 73 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 74 through 97 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 98 through 106 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 107 through 129 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 130 through 217 )D0
24X-RAY DIFFRACTION24chain 'W' and (resid 244 through 254 )W0
25X-RAY DIFFRACTION25chain 'X' and (resid 244 through 255 )X0
26X-RAY DIFFRACTION26chain 'Y' and (resid 244 through 254 )Y0
27X-RAY DIFFRACTION27chain 'Z' and (resid 244 through 254 )Z0

+
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