[English] 日本語
Yorodumi
- PDB-2jkr: AP2 CLATHRIN ADAPTOR CORE with Dileucine peptide RM(phosphoS)QIKRLLSE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jkr
TitleAP2 CLATHRIN ADAPTOR CORE with Dileucine peptide RM(phosphoS)QIKRLLSE
Components
  • (AP-2 COMPLEX SUBUNIT ...) x 4
  • CD4 PEPTIDE
KeywordsENDOCYTOSIS / ALTERNATIVE SPLICING / PHOSPHOPROTEIN / PHOSPHORYLATION / PROTEIN TRANSPORT / ADAPTOR / MEMBRANE / TRANSPORT / COATED PIT / CELL MEMBRANE / LIPID-BINDING
Function / homology
Function and homology information


Gap junction degradation / Formation of annular gap junctions / Nef Mediated CD8 Down-regulation / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / LDL clearance / Retrograde neurotrophin signalling ...Gap junction degradation / Formation of annular gap junctions / Nef Mediated CD8 Down-regulation / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD4 / clathrin adaptor complex / MHC class II antigen presentation / extrinsic component of presynaptic endocytic zone membrane / Trafficking of GluR2-containing AMPA receptors / VLDLR internalisation and degradation / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / Recycling pathway of L1 / regulation of vesicle size / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / maintenance of protein location in cell / cellular response to ionomycin / response to methamphetamine hydrochloride / Retrograde neurotrophin signalling / Recycling pathway of L1 / T cell selection / clathrin-coated endocytic vesicle / Cargo recognition for clathrin-mediated endocytosis / membrane coat / Cargo recognition for clathrin-mediated endocytosis / clathrin coat assembly / LDL clearance / Clathrin-mediated endocytosis / MHC class II protein binding / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / clathrin-cargo adaptor activity / vesicle budding from membrane / interleukin-15-mediated signaling pathway / clathrin-dependent endocytosis / cellular response to granulocyte macrophage colony-stimulating factor stimulus / signal sequence receptor activity / MHC class II antigen presentation / positive regulation of monocyte differentiation / Alpha-defensins / Nef Mediated CD4 Down-regulation / coronary vasculature development / positive regulation of protein localization to membrane / endolysosome membrane / neurotransmitter secretion / regulation of T cell activation / response to vitamin D / regulation of hematopoietic stem cell differentiation / Other interleukin signaling / ventricular septum development / aorta development / low-density lipoprotein particle receptor binding / extracellular matrix structural constituent / T cell receptor complex / enzyme-linked receptor protein signaling pathway / clathrin binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Trafficking of GluR2-containing AMPA receptors / Recycling pathway of L1 / Generation of second messenger molecules / macrophage differentiation / T cell differentiation / positive regulation of receptor internalization / immunoglobulin binding / Co-inhibition by PD-1 / EPH-ephrin mediated repulsion of cells / positive regulation of calcium ion transport into cytosol / Binding and entry of HIV virion / positive regulation of endocytosis / negative regulation of protein localization to plasma membrane / synaptic vesicle endocytosis / positive regulation of interleukin-2 production / coreceptor activity / vesicle-mediated transport / Neutrophil degranulation / clathrin-coated pit / MHC class II antigen presentation / positive regulation of T cell proliferation / phosphatidylinositol binding / positive regulation of calcium-mediated signaling / secretory granule / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase binding / VLDLR internalisation and degradation / protein serine/threonine kinase binding / kidney development
Similarity search - Function
Beta-Lactamase - #60 / Mu homology domain, subdomain B / AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / CD4, extracellular ...Beta-Lactamase - #60 / Mu homology domain, subdomain B / AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Beta2-adaptin appendage, C-terminal sub-domain / AP-1/2/4 complex subunit beta / Adaptor protein complex, sigma subunit / : / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / AP complex subunit beta / Clathrin adaptor complexes medium chain signature 1. / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family / Clathrin adaptor complex small chain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / AP-2 complex subunit mu, C-terminal superfamily / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Longin-like domain superfamily / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Immunoglobulin / Immunoglobulin domain / Beta-Lactamase / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Alpha Horseshoe / Armadillo-like helical / Immunoglobulin subtype / Immunoglobulin / Armadillo-type fold / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
cDNA, FLJ79547, highly similar to T-cell surface glycoprotein CD4 / T-cell surface glycoprotein CD4 / AP-2 complex subunit alpha-2 / AP-2 complex subunit sigma / AP-2 complex subunit beta / AP-2 complex subunit mu
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
RATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsOwen, D.J. / McCoy, A.J. / Kelly, B.T. / Evans, P.R.
CitationJournal: Nature / Year: 2008
Title: A Structural Explanation for the Binding of Endocytic Dileucine Motifs by the Ap2 Complex.
Authors: Kelly, B.T. / Mccoy, A.J. / Spaete, K. / Miller, S.E. / Evans, P.R. / Hoening, S. / Owen, D.J.
History
DepositionAug 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AP-2 COMPLEX SUBUNIT ALPHA-2
B: AP-2 COMPLEX SUBUNIT BETA-1
E: AP-2 COMPLEX SUBUNIT BETA-1
I: AP-2 COMPLEX SUBUNIT SIGMA-1
L: AP-2 COMPLEX SUBUNIT ALPHA-2
M: AP-2 COMPLEX SUBUNIT MU-1
P: CD4 PEPTIDE
Q: CD4 PEPTIDE
S: AP-2 COMPLEX SUBUNIT SIGMA-1
U: AP-2 COMPLEX SUBUNIT MU-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)412,87541
Polymers409,89710
Non-polymers2,97831
Water34219
1
A: AP-2 COMPLEX SUBUNIT ALPHA-2
B: AP-2 COMPLEX SUBUNIT BETA-1
M: AP-2 COMPLEX SUBUNIT MU-1
P: CD4 PEPTIDE
S: AP-2 COMPLEX SUBUNIT SIGMA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,29319
Polymers204,9495
Non-polymers1,34514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23280 Å2
ΔGint-260.1 kcal/mol
Surface area68870 Å2
MethodPISA
2
E: AP-2 COMPLEX SUBUNIT BETA-1
I: AP-2 COMPLEX SUBUNIT SIGMA-1
L: AP-2 COMPLEX SUBUNIT ALPHA-2
Q: CD4 PEPTIDE
U: AP-2 COMPLEX SUBUNIT MU-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,58222
Polymers204,9495
Non-polymers1,63317
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24020 Å2
ΔGint-303.8 kcal/mol
Surface area68680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.900, 169.900, 321.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 3:623 )
211CHAIN L AND (RESSEQ 3:623 )
112CHAIN B AND (RESSEQ 12:582 )
212CHAIN E AND (RESSEQ 12:582 )
113CHAIN M AND (RESSEQ 1:141 OR RESSEQ 159:222 OR RESSEQ 232:435 )
213CHAIN U AND (RESSEQ 1:141 OR RESSEQ 159:222 OR RESSEQ 232:435 )
114CHAIN S AND (RESSEQ 1:142 )
214CHAIN I AND (RESSEQ 1:142 )
115CHAIN P AND (RESSEQ 2:10 )
215CHAIN Q AND (RESSEQ 2:10 )

NCS ensembles :
ID
1
2
3
4
5

NCS oper: (Code: given
Matrix: (0.005, 0.998, 0.062), (0.998, -0.009, 0.056), (0.057, 0.062, -0.996)
Vector: 6.985, 2.861, -160.492)

-
Components

-
AP-2 COMPLEX SUBUNIT ... , 4 types, 8 molecules ALBEISMU

#1: Protein AP-2 COMPLEX SUBUNIT ALPHA-2 / AP2 / ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA-2 SUBUNIT / ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT ...AP2 / ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA-2 SUBUNIT / ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT ALPHA-2 / ALPHA2-ADAPTIN / PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN ALPHA C SUBUNIT / ALPHA-ADAPTIN C / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 ALPHA-C LARGE CHAIN / 100 KDA COATED VESICLE PROTEIN C


Mass: 69786.406 Da / Num. of mol.: 2 / Fragment: ALPHA CHAIN, RESIDUES 1-620
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PMW172K / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17427
#2: Protein AP-2 COMPLEX SUBUNIT BETA-1 / AP2 / ADAPTER-RELATED PROTEIN COMPLEX 2 BETA-1 SUBUNIT / BETA2-ADAPTIN / BETA-ADAPTIN / PLASMA ...AP2 / ADAPTER-RELATED PROTEIN COMPLEX 2 BETA-1 SUBUNIT / BETA2-ADAPTIN / BETA-ADAPTIN / PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN BETA SUBUNIT / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 BETA LARGE CHAIN / AP105B


Mass: 66953.195 Da / Num. of mol.: 2 / Fragment: BETA2 CHAIN, RESIDUES 1-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMW172H6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63010
#3: Protein AP-2 COMPLEX SUBUNIT SIGMA-1 / AP2 / ADAPTER-RELATED PROTEIN COMPLEX 2 SIGMA-1 SUBUNIT / SIGMA2-ADAPTIN / SIGMA-ADAPTIN 3B / ...AP2 / ADAPTER-RELATED PROTEIN COMPLEX 2 SIGMA-1 SUBUNIT / SIGMA2-ADAPTIN / SIGMA-ADAPTIN 3B / PLASMA MEMBRANE ADAPTOR AP-2 17 KDA PROTEIN / CLATHRIN ASSEMBLY PROTEIN 2 SMALL CHAIN / CLATHRIN COAT ASSEMBLY PROTEIN AP17 / CLATHRIN COAT-ASSOCIATED PROTEIN AP17


Mass: 17038.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PMW172K / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62743
#4: Protein AP-2 COMPLEX SUBUNIT MU-1 / AP2 / MU2-ADAPTIN / AP-2 MU-2 CHAIN / PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN / CLATHRIN ...AP2 / MU2-ADAPTIN / AP-2 MU-2 CHAIN / PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 MEDIUM CHAIN / CLATHRIN COAT ASSEMBLY PROTEIN AP50 / CLATHRIN COAT-ASSOCIATED PROTEIN AP50


Mass: 49726.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PMW172H6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P84092

-
Protein/peptide , 1 types, 2 molecules PQ

#5: Protein/peptide CD4 PEPTIDE / CDNA / FLJ79547 / HIGHLY SIMILAR TO T-CELL SURFACE GLYCOPROTEIN CD4


Mass: 1443.629 Da / Num. of mol.: 2 / Fragment: RESIDUES 252-262 / Source method: obtained synthetically
Details: RMS(P)EIKRLLSE. RESIDUE 3 IS PHOSPHOSERINE THOUGH NO PHOSPHORYL GROUP WAS VISIBLE IN THE STRUCTURE
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: B0AZV7, UniProt: P01730*PLUS

-
Non-polymers , 2 types, 50 molecules

#6: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsSEQUENCE OF CHAINS A AND L IS FROM MOUSE BUT HAS GLU INSERTED AT POSITION 272

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 57.96 % / Description: NONE
Crystal growpH: 6.5
Details: 1.7-2.2M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH6 .5 AND 5MM DTT FROM A MIXTURE OF 10MG/ML AP2 CORE AND 7MG/ML PEPTIDE. CRYOPROTECTED WITH 1.8-2.3M AMMONIUM SULPHATE, 100MM SODIUM CITRATE ...Details: 1.7-2.2M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH6 .5 AND 5MM DTT FROM A MIXTURE OF 10MG/ML AP2 CORE AND 7MG/ML PEPTIDE. CRYOPROTECTED WITH 1.8-2.3M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH 6.5, 17% GLYCEROL AND 7MG/ ML CD4 DILEUCINE PEPTIDE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: May 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3→51 Å / Num. obs: 96683 / % possible obs: 100 % / Observed criterion σ(I): -9 / Redundancy: 8.8 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 9 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 1.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VGL

2vgl


Resolution: 2.98→50.95 Å / SU ML: 0.44 / σ(F): 1.23 / Phase error: 27.79 / Stereochemistry target values: ML
Details: 28 TLS GROUPS. THE PHOSPHATE OF THE PHOSPHOSERINE RESIDUES P3 AND Q3 WERE NOT VISIBLE, SO THE RESIDUE WAS MODELLED AS SERINE
RfactorNum. reflection% reflection
Rfree0.26 9168 5 %
Rwork0.199 --
obs0.202 183747 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.75 Å2 / ksol: 0.33 e/Å3
Refinement stepCycle: LAST / Resolution: 2.98→50.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27946 0 155 19 28120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128556
X-RAY DIFFRACTIONf_angle_d1.37738646
X-RAY DIFFRACTIONf_dihedral_angle_d23.57317614
X-RAY DIFFRACTIONf_chiral_restr0.0914472
X-RAY DIFFRACTIONf_plane_restr0.0054892
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4885X-RAY DIFFRACTIONPOSITIONAL
12L4885X-RAY DIFFRACTIONPOSITIONAL0.054
21B4527X-RAY DIFFRACTIONPOSITIONAL
22E4527X-RAY DIFFRACTIONPOSITIONAL0.05
31M3288X-RAY DIFFRACTIONPOSITIONAL
32U3288X-RAY DIFFRACTIONPOSITIONAL0.046
41S1200X-RAY DIFFRACTIONPOSITIONAL
42I1200X-RAY DIFFRACTIONPOSITIONAL0.048
51P73X-RAY DIFFRACTIONPOSITIONAL
52Q73X-RAY DIFFRACTIONPOSITIONAL0.042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9782-3.0120.39162930.3645640X-RAY DIFFRACTION97
3.012-3.04750.3972960.33755855X-RAY DIFFRACTION100
3.0475-3.08460.34233050.32475834X-RAY DIFFRACTION100
3.0846-3.12370.38073020.32315817X-RAY DIFFRACTION100
3.1237-3.16480.37052770.30915873X-RAY DIFFRACTION100
3.1648-3.20810.36942860.2955848X-RAY DIFFRACTION100
3.2081-3.25390.34983300.29825806X-RAY DIFFRACTION100
3.2539-3.30250.39422840.28115816X-RAY DIFFRACTION100
3.3025-3.35410.32562410.2635863X-RAY DIFFRACTION100
3.3541-3.40910.34473120.26345878X-RAY DIFFRACTION100
3.4091-3.46780.30683250.24655802X-RAY DIFFRACTION100
3.4678-3.53090.29963370.22725799X-RAY DIFFRACTION100
3.5309-3.59880.28072950.20745821X-RAY DIFFRACTION100
3.5988-3.67220.28393480.20775782X-RAY DIFFRACTION100
3.6722-3.7520.25953130.19275857X-RAY DIFFRACTION100
3.752-3.83930.26672740.17685832X-RAY DIFFRACTION100
3.8393-3.93530.27083240.17565837X-RAY DIFFRACTION100
3.9353-4.04160.20952800.1585868X-RAY DIFFRACTION100
4.0416-4.16050.24362970.15865777X-RAY DIFFRACTION100
4.1605-4.29470.22883300.14725844X-RAY DIFFRACTION100
4.2947-4.44810.19942910.13125834X-RAY DIFFRACTION100
4.4481-4.62610.17553420.12245760X-RAY DIFFRACTION100
4.6261-4.83650.20482670.13825877X-RAY DIFFRACTION100
4.8365-5.09130.22952910.14625827X-RAY DIFFRACTION100
5.0913-5.40990.24383150.15415840X-RAY DIFFRACTION100
5.4099-5.82710.24383720.16895753X-RAY DIFFRACTION100
5.8271-6.41250.27022950.17315820X-RAY DIFFRACTION100
6.4125-7.3380.24153130.16965836X-RAY DIFFRACTION100
7.338-9.23620.1723430.12685791X-RAY DIFFRACTION100
9.2362-50.96110.16112900.16535792X-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)
11.3979-0.4871-1.16950.41150.18960.92440.57280.1508-0.3755-0.274-0.0735-0.08130.25260.8258-0.27840.62370.1645-0.27181.01150.01540.77681.1375-24.6458-97.352
21.7507-0.6169-0.95280.46180.29571.29640.4661-0.27580.2028-0.0290.1067-0.4784-0.12190.1249-0.46310.2835-0.04570.03880.2809-0.05610.498873.0662-4.1883-107.4668
34.7861-0.8613-1.6220.7166-0.36860.28460.76661.69220.9211-0.7854-0.5567-0.4753-0.6777-0.3769-0.22870.25960.20520.15480.58240.21770.2348.71841.704-118.5513
42.2981-0.2301-1.30910.99481.17992.13610.12890.4202-0.2870.1036-0.305-0.0272-0.1116-0.38030.12670.1643-0.0183-0.0310.2699-0.06170.08329.4186-8.1405-98.005
51.90140.0486-1.14831.12861.5634-1.2848-0.4165-0.102-0.00810.3680.1277-0.0971-0.09230.07630.18990.55790.1455-0.08370.3820.05670.04715.0284-0.5358-54.7729
60.9429-0.51370.77421.08010.1994-3.34940.7190.4488-0.3502-0.8104-0.80390.0480.23720.19450.0330.36740.4745-0.6170.02520.8954-0.745630.21425.3706-88.5266
73.049-0.00350.31240.47120.14410.26910.64640.0449-1.06180.1143-0.67820.3507-0.3008-0.1605-0.00060.5851-0.2091-0.04180.7488-0.191.059667.8467-46.5462-83.0508
80.91050.0887-0.4512-0.70010.01650.9763-0.29430.0986-0.59110.16790.04040.1017-0.0604-0.05250.20150.53170.0148-0.04180.3198-0.08420.553355.3141-52.0918-58.2339
9-0.0629-0.5540.57522.09330.79161.5757-0.0951-0.09520.16020.00140.2234-0.42690.1634-0.13720.02020.29730.0671-0.19080.04370.05490.324152.9595-16.2654-37.402
101.702-0.8694-1.35730.8040.8576-0.0397-0.00430.0040.14470.14990.1782-0.13180.0134-0.0475-0.08510.4563-0.0283-0.21190.23730.05540.151229.145116.5102-48.4585
111.7532-0.5229-1.21080.7455-1.15221.21170.2901-0.2806-0.15710.29750.15930.9488-0.19560.1203-0.32050.4496-0.1338-0.00170.32110.02460.514340.8097-22.4292-43.4284
121.6178-0.49730.32380.7797-0.51870.80920.19050.3609-0.26030.1812-0.0081-0.2244-0.1181-0.1318-0.14250.36150.042-0.19150.2913-0.01350.416760.5843-29.2918-61.9924
131.1112-0.46881.37830.18230.10431.44980.00020.27830.23930.0994-0.123-0.16980.11610.2560.09270.4021-0.0685-0.11520.41970.14470.393253.70714.8797-70.8161
142.8539-0.057-1.25890.38961.13150.86090.1005-0.429-0.3942-0.34820.1062-0.04510.02810.1148-0.15360.38080.013-0.05710.3080.02330.266357.0681-17.3492-101.2189
150.13060.5086-0.35120.65031.1506-0.1725-0.0608-0.0127-0.20050.56250.06840.2717-0.4156-0.0101-0.01860.5670.20920.10760.19570.25340.404-23.50178.1872-59.7796
160.6949-0.6894-0.52361.36860.76431.50650.00770.03590.2584-0.03540.3777-0.4167-0.04230.08-0.31190.1397-0.06620.03620.1726-0.01360.2961-3.822269.2143-48.8999
170.7297-0.5557-0.27781.49571.43752.8217-0.7695-0.8087-0.2970.81220.881-0.13810.94390.2259-0.16720.43360.1056-0.23280.0404-0.2486-0.20181.134744.1123-39.1287
181.2283-0.1305-0.91.71890.68921.1289-0.36770.0621-0.08820.32170.09920.09570.41980.15780.20930.3671-0.01550.05770.1970.04920.0559-7.442826.3393-61.5406
192.1135-1.1347-1.26562.06750.6304-1.69050.19410.2998-0.08140.0851-0.35780.0487-0.217-0.06380.08510.43410.10050.01930.48380.07010.02522.901414.7442-105.0478
20-0.8858-0.145-1.90961.9407-0.5779-3.3138-0.32610.0897-0.13031.05340.18820.1218-0.27371.35770.19870.43880.0784-0.39870.48540.098-0.182826.63227.3865-68.7498
212.54611.0449-0.4632-0.90220.90220.4119-1.01060.4564-0.9398-0.10230.30970.39480.0250.29350.49160.9314-0.23510.01770.80340.05011.2685-44.435766.0929-76.0369
22-0.473-0.251-0.18310.99360.90751.3751-0.07780.0335-0.03140.1569-0.1870.81420.09880.04270.19770.28970.05560.13980.53310.05250.4539-48.825454.9892-101.7502
231.8030.0112-0.83660.1264-0.48160.83570.1562-0.0750.147-0.0357-0.022-0.02160.0546-0.1639-0.09510.2070.10530.0450.30390.21010.2956-12.035253.544-120.9226
241.0904-0.2726-0.82451.67831.5007-0.48880.17020.40960.1464-0.1174-0.0473-0.3012-0.1497-0.016-0.07930.28130.0512-0.00030.30590.17990.124520.10328.9414-109.635
256.64912.03860.171.62910.31782.357-0.05010.2088-2.0182-0.16660.3924-0.3015-0.51430.1852-0.15060.363-0.2080.13590.5325-0.03650.7368-18.539741.1319-115.8811
260.5803-0.46030.10041.1594-0.60491.1153-0.01470.16140.35230.48350.14780.11820.05520.02580.07220.22540.0440.1270.21440.19390.2245-26.095760.0578-96.6076
270.6043-0.38490.33350.1575-0.2656-0.3765-0.07950.11370.03390.31670.122-0.0418-0.2762-0.0448-0.04250.43430.0055-0.02660.31460.07490.14217.499952.1163-86.5212
280.4308-0.578-0.74341.54680.37040.36290.2232-0.15980.0725-0.5117-0.0260.2333-0.12750.1307-0.13720.3225-0.03550.02530.34370.05810.1367-16.610853.958-57.0629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 1:50)
2X-RAY DIFFRACTION2CHAIN A AND RESID 51:186)
3X-RAY DIFFRACTION3CHAIN A AND RESID 187:245)
4X-RAY DIFFRACTION4CHAIN A AND RESID 246:457)
5X-RAY DIFFRACTION5CHAIN A AND RESID 458:610)
6X-RAY DIFFRACTION6CHAIN A AND RESID 611:999)
7X-RAY DIFFRACTION7CHAIN B AND RESID 1:51)
8X-RAY DIFFRACTION8CHAIN B AND RESID 52:206)
9X-RAY DIFFRACTION9CHAIN B AND RESID 207:414)
10X-RAY DIFFRACTION10CHAIN B AND RESID 415:549)
11X-RAY DIFFRACTION11CHAIN B AND RESID 550:999)
12X-RAY DIFFRACTION12CHAIN M AND RESID 1:159)
13X-RAY DIFFRACTION13CHAIN M AND RESID 160:435)
14X-RAY DIFFRACTION14CHAIN S AND RESID 1:142) OR CHAIN P
15X-RAY DIFFRACTION15CHAIN L AND RESID 1:50)
16X-RAY DIFFRACTION16CHAIN L AND RESID 51:186)
17X-RAY DIFFRACTION17CHAIN L AND RESID 187:245)
18X-RAY DIFFRACTION18CHAIN L AND RESID 246:457)
19X-RAY DIFFRACTION19CHAIN L AND RESID 458:610)
20X-RAY DIFFRACTION20CHAIN L AND RESID 611:999)
21X-RAY DIFFRACTION21CHAIN E AND RESID 1:51)
22X-RAY DIFFRACTION22CHAIN E AND RESID 52:206)
23X-RAY DIFFRACTION23CHAIN E AND RESID 207:414)
24X-RAY DIFFRACTION24CHAIN E AND RESID 415:549)
25X-RAY DIFFRACTION25CHAIN E AND RESID 550:999)
26X-RAY DIFFRACTION26CHAIN U AND RESID 1:159)
27X-RAY DIFFRACTION27CHAIN U AND RESID 160:435)
28X-RAY DIFFRACTION28CHAIN I AND RESID 1:142) OR CHAIN Q

+
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