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- PDB-2xa7: AP2 clathrin adaptor core in active complex with cargo peptides -

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Basic information

Entry
Database: PDB / ID: 2xa7
TitleAP2 clathrin adaptor core in active complex with cargo peptides
Components
  • (AP-2 COMPLEX SUBUNIT ...) x 3
  • ADAPTOR-RELATED PROTEIN COMPLEX 2, ALPHA 2 SUBUNIT
  • TGN38 CARGO PEPTIDE
KeywordsPROTEIN TRANSPORT / PHOSPHOPROTEIN / ENDOCYTOSIS / CELL MEMBRANE / LIPID-BINDING
Function / homology
Function and homology information


Gap junction degradation / Formation of annular gap junctions / secretory vesicle / 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 ...Gap junction degradation / Formation of annular gap junctions / secretory vesicle / 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 / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / VLDLR internalisation and degradation / clathrin adaptor complex / MHC class II antigen presentation / extrinsic component of presynaptic endocytic zone membrane / Recycling pathway of L1 / regulation of vesicle size / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Retrograde neurotrophin signalling / Recycling pathway of L1 / Cargo recognition for clathrin-mediated endocytosis / clathrin-coated endocytic vesicle / membrane coat / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin coat assembly / LDL clearance / Clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / clathrin-cargo adaptor activity / vesicle budding from membrane / clathrin-dependent endocytosis / MHC class II antigen presentation / signal sequence binding / Nef Mediated CD4 Down-regulation / coronary vasculature development / positive regulation of protein localization to membrane / endolysosome membrane / neurotransmitter secretion / Neutrophil degranulation / ventricular septum development / aorta development / low-density lipoprotein particle receptor binding / clathrin binding / Trafficking of GluR2-containing AMPA receptors / Recycling pathway of L1 / positive regulation of receptor internalization / EPH-ephrin mediated repulsion of cells / positive regulation of endocytosis / negative regulation of protein localization to plasma membrane / synaptic vesicle endocytosis / vesicle-mediated transport / clathrin-coated pit / MHC class II antigen presentation / phosphatidylinositol binding / VLDLR internalisation and degradation / protein serine/threonine kinase binding / kidney development / clathrin-coated endocytic vesicle membrane / intracellular protein transport / receptor internalization / cytoplasmic side of plasma membrane / kinase binding / disordered domain specific binding / terminal bouton / endocytic vesicle membrane / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein-containing complex assembly / cytoplasmic vesicle / Potential therapeutics for SARS / transmembrane transporter binding / postsynapse / protein domain specific binding / synapse / lipid binding / protein kinase binding / protein-containing complex binding / glutamatergic synapse / membrane / plasma membrane / cytosol
Similarity search - Function
Beta-Lactamase - #60 / 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 / Beta2-adaptin appendage, C-terminal sub-domain / AP-1/2/4 complex subunit beta ...Beta-Lactamase - #60 / 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 / 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 / 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 / Beta-Lactamase / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AP-2 complex subunit alpha-2 / AP-2 complex subunit sigma / AP-2 complex subunit beta / AP-2 complex subunit mu / AP-2 complex subunit alpha
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
HOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.1 Å
AuthorsJackson, L.P. / Kelly, B.T. / McCoy, A.J. / Evans, P.R. / Owen, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: A Large Scale Conformational Change Couples Membrane Recruitment to Cargo Binding in the Ap2 Clathrin Adaptor Complex
Authors: Jackson, L.P. / Kelly, B.T. / Mccoy, A.J. / Gaffry, T. / James, L.C. / Collins, B.M. / Honing, S. / Evans, P.R. / Owen, D.J.
History
DepositionMar 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADAPTOR-RELATED PROTEIN COMPLEX 2, ALPHA 2 SUBUNIT
B: AP-2 COMPLEX SUBUNIT BETA
M: AP-2 COMPLEX SUBUNIT MU,
P: TGN38 CARGO PEPTIDE
S: AP-2 COMPLEX SUBUNIT SIGMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,12010
Polymers205,6395
Non-polymers4805
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20160 Å2
ΔGint-154.2 kcal/mol
Surface area76310 Å2
MethodPISA
2
A: ADAPTOR-RELATED PROTEIN COMPLEX 2, ALPHA 2 SUBUNIT
B: AP-2 COMPLEX SUBUNIT BETA
M: AP-2 COMPLEX SUBUNIT MU,
S: AP-2 COMPLEX SUBUNIT SIGMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,3119
Polymers204,8304
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19230 Å2
ΔGint-149.3 kcal/mol
Surface area76070 Å2
MethodPISA
3
P: TGN38 CARGO PEPTIDE


  • defined by author&software
  • 809 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)8091
Polymers8091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)255.316, 255.316, 156.754
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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AP-2 COMPLEX SUBUNIT ... , 3 types, 3 molecules BMS

#2: Protein AP-2 COMPLEX SUBUNIT BETA / ADAPTER-RELATED PROTEIN COMPLEX 2 BETA SUBUNIT / ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT BETA / BETA-2- ...ADAPTER-RELATED PROTEIN COMPLEX 2 BETA SUBUNIT / ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT BETA / BETA-2-ADAPTIN / BETA-ADAPTIN / PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN BETA SUBUNIT / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 BETA LARGE CHAIN / AP105B / AP2


Mass: 67091.344 Da / Num. of mol.: 1 / Fragment: BETA CHAIN, RESIDUES 1-592
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMW172K / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P63010
#3: Protein AP-2 COMPLEX SUBUNIT MU, / ADAPTER-RELATED PROTEIN COMPLEX 2 MU SUBUNIT / ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT MU / MU2- ...ADAPTER-RELATED PROTEIN COMPLEX 2 MU SUBUNIT / ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT MU / MU2-ADAPTIN AP-2 MU 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 / AP2


Mass: 51044.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PMW172K / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P84092
#5: Protein AP-2 COMPLEX SUBUNIT SIGMA / ADAPTER-RELATED PROTEIN COMPLEX 2 SIGMA SUBUNIT / ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT SIGMA / ...ADAPTER-RELATED PROTEIN COMPLEX 2 SIGMA SUBUNIT / ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT SIGMA / 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.: 1
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)PLYSS / References: UniProt: P62743

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Protein / Protein/peptide / Non-polymers , 3 types, 7 molecules AP

#1: Protein ADAPTOR-RELATED PROTEIN COMPLEX 2, ALPHA 2 SUBUNIT / AP2


Mass: 69656.297 Da / Num. of mol.: 1 / Fragment: ALPHA CHAIN, RESIDUES 1-621
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PMW172K / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q66HM2, UniProt: P18484*PLUS
#4: Protein/peptide TGN38 CARGO PEPTIDE


Mass: 808.860 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: HEXAPEPTIDE INTERNALISATION SIGNAL MOTIF (DYQRLN) FROM TGN38
Source: (synth.) HOMO SAPIENS (human)
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4

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Details

Sequence detailsMYC TAG MEQKLISEEDL INSERTED INTO MU2 CHAIN

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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: 4.78 Å3/Da / Density % sol: 74.28 % / Description: NONE
Crystal growpH: 6.5
Details: 0.6-0.8M LISO4, 0.6-0.7M NH4SO4, 100MM NA CITRATE PH 6.5; CRYOPROTECTANT 20% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 2006 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.1→64 Å / Num. obs: 66846 / % possible obs: 96.7 % / Observed criterion σ(I): -10 / Redundancy: 5.5 % / Biso Wilson estimate: 73 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 5.7
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.3 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 3.1→127.88 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.898 / SU B: 49.154 / SU ML: 0.396 / Cross valid method: THROUGHOUT / ESU R: 1.106 / ESU R Free: 0.43
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DATA ARE HIGHLY ANISOTROPIC AND LOW RESOLUTION, SO THE DETAILED CONFORMATIONS OF SIDE CHAINS IS UNRELIABLE. THE MYC TAG IN THE MU2 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DATA ARE HIGHLY ANISOTROPIC AND LOW RESOLUTION, SO THE DETAILED CONFORMATIONS OF SIDE CHAINS IS UNRELIABLE. THE MYC TAG IN THE MU2 CHAIN (RESIDUES M 237-242) IS BOUND IN THE ACIDIC DILEUCINE MOTIF BINDING SITE ON THE SIGMA2 CHAIN OF A CRYSTALLOGRAPHICALLY RELATED MOLECULE, MIMICKING THE BINDING OF THIS CARGO MOTIF. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28459 3376 5.1 %RANDOM
Rwork0.23639 ---
obs0.23884 63145 96.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.93 Å2-2.97 Å20 Å2
2---5.93 Å20 Å2
3---8.9 Å2
Refinement stepCycle: LAST / Resolution: 3.1→127.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14112 0 25 0 14137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.02315140
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.051.97519459
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.04451761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.00224.482647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.294152665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1961591
X-RAY DIFFRACTIONr_chiral_restr0.1440.22259
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110590
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6631.59602
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.028214361
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.51635538
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5694.55098
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 251 -
Rwork0.358 4487 -
obs--92.05 %
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)
10.4083-1.13470.75015.3628-3.7942.7551-0.0436-0.3701-0.2939-0.10760.26430.20810.2903-0.1276-0.22070.93040.037-0.1451.715-0.0221.612771.889-6.27429.093
20.33770.9074-0.50382.869-1.64642.49420.1533-0.3382-0.02580.5616-0.2278-0.2440.91830.74890.07451.38140.369-0.66481.97280.11491.284252.365-9.61845.945
35.14323.9719-1.67878.6987-1.74454.33610.4656-1.3850.9171.99650.196-0.74510.22770.5134-0.66171.2101-0.0776-0.53871.3734-0.25160.767126.4951.20647.324
42.05751.0261.95355.44762.6863.98680.0924-0.5434-0.12510.4457-0.0528-0.5058-0.1477-0.1754-0.03960.1667-0.0289-0.10410.29010.04090.084117.959-2.62919.446
52.8616-0.75410.28557.54220.15922.69210.02030.1655-0.7492-0.3929-0.1680.22060.4036-0.08890.14770.1212-0.02240.03540.2517-0.08210.219310.192-40.563-3.647
60.57241.3211-4.00694.7693-6.835731.50710.3226-0.2617-0.19991.70150.0042-1.7282-0.34512.4684-0.32681.2764-0.0293-0.82880.6798-0.33681.006920.123-23.01217.745
79.35061.2726-0.56441.58252.87698.26470.3563-0.86560.81660.32450.0358-0.4114-0.32920.7626-0.39210.6768-0.1376-0.05150.3396-0.04161.135548.2468.515-1.28
80.5385-0.0947-0.86653.66251.46014.45410.15370.55970.2909-0.9166-0.25440.5326-0.2491-0.42710.10070.65070.20.130.88150.13910.559136.926-4.587-24.486
92.6408-0.3894-0.78393.3914-1.65883.1787-0.00160.3156-0.6694-0.5432-0.0691-0.43450.46050.07220.07070.4040.11180.11420.4186-0.16510.369645.904-42.997-12.56
106.6254-2.24660.04563.84650.41592.5001-0.2134-0.6882-0.94210.51720.1308-0.23220.47110.13460.08260.53390.00450.07580.23650.18410.295620.375-54.32512.302
1113.478-6.61810.586910.68811.20585.1424-0.18540.7906-0.0218-0.03360.28220.12470.6516-0.3441-0.09690.233-0.03930.05940.4331-0.13430.19533.773-36.721-11.433
125.92113.1581-2.39776.6121-0.78154.8118-0.09040.19550.6369-0.1209-0.0176-0.6507-0.00820.06890.10790.29070.15870.02860.2955-0.04140.406949.56-13.391-9.581
132.57070.5336-0.59212.7338-0.23911.81270.1275-0.5788-0.11620.4732-0.1986-0.30930.14860.34020.07110.65530.13780.23470.9681-0.11450.754772.143-35.715-12.428
144.07031.9884-0.46973.74610.90026.22040.1493-0.8349-1.1910.46480.1337-0.57240.29450.7724-0.2830.47610.1517-0.29520.71750.0120.576545.087-0.72828.126
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 50
2X-RAY DIFFRACTION2A51 - 186
3X-RAY DIFFRACTION3A187 - 245
4X-RAY DIFFRACTION4A246 - 457
5X-RAY DIFFRACTION5A458 - 610
6X-RAY DIFFRACTION6A611 - 621
7X-RAY DIFFRACTION7B4 - 51
8X-RAY DIFFRACTION8B52 - 206
9X-RAY DIFFRACTION9B207 - 414
10X-RAY DIFFRACTION10B415 - 549
11X-RAY DIFFRACTION11B550 - 582
12X-RAY DIFFRACTION12M1 - 157
13X-RAY DIFFRACTION13M158 - 435
14X-RAY DIFFRACTION13P1 - 6
15X-RAY DIFFRACTION14S1 - 142

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  • 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

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