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- PDB-7ow3: Crystal structure of HLA-A*11:01 in complex with KRAS peptide (VV... -

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Basic information

Entry
Database: PDB / ID: 7ow3
TitleCrystal structure of HLA-A*11:01 in complex with KRAS peptide (VVVGAGGVGK)
Components
  • Beta-2-microglobulin
  • KRAS peptide (VVVGAGGVGK)
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / HLA / KRAS
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / tertiary granule membrane / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling ...antigen processing and presentation of peptide antigen via MHC class I / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / tertiary granule membrane / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / positive regulation of endothelial cell proliferation / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Ras activation upon Ca2+ influx through NMDA receptor / Constitutive Signaling by Overexpressed ERBB2 / negative regulation of receptor binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / VEGFR2 mediated cell proliferation / transferrin transport / small monomeric GTPase / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCERI mediated MAPK activation / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / Signaling by SCF-KIT / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / T cell mediated cytotoxicity / MAP2K and MAPK activation / positive regulation of T cell cytokine production / Signaling by ERBB2 ECD mutants / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / Signaling by ERBB2 KD Mutants / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation
Similarity search - Function
Small GTPase, Ras-type / Small GTPase Ras domain profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases ...Small GTPase, Ras-type / Small GTPase Ras domain profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Rab subfamily of small GTPases / MHC classes I/II-like antigen recognition protein / : / Small GTP-binding protein domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I antigen / GTPase NRas / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsColes, C.H. / Karuppiah, V. / Robinson, R.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Therapeutic high affinity T cell receptor targeting a KRASG12D cancer neoantigen
Authors: Poole, A. / Karuppiah, V. / Hartt, A. / Haidar, J.N. / Moureau, S. / Dobrzycki, T. / Hayes, C. / Rowley, C. / Dias, J. / Harper, S. / Barnbrook, K. / Hock, M. / Coles, C. / Yang, W. / ...Authors: Poole, A. / Karuppiah, V. / Hartt, A. / Haidar, J.N. / Moureau, S. / Dobrzycki, T. / Hayes, C. / Rowley, C. / Dias, J. / Harper, S. / Barnbrook, K. / Hock, M. / Coles, C. / Yang, W. / Aleksic, M. / Lin, A.B. / Robinson, R. / Dukes, J.D. / Liddy, N. / Van der Kamp, M. / Plowman, G.D. / Vuidepot, A. / Cole, D.K. / Whale, A.D. / Chillakuri, C.
History
DepositionJun 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: KRAS peptide (VVVGAGGVGK)
D: MHC class I antigen
E: Beta-2-microglobulin
F: KRAS peptide (VVVGAGGVGK)
G: MHC class I antigen
H: Beta-2-microglobulin
I: KRAS peptide (VVVGAGGVGK)
J: MHC class I antigen
K: Beta-2-microglobulin
L: KRAS peptide (VVVGAGGVGK)


Theoretical massNumber of molelcules
Total (without water)178,31012
Polymers178,31012
Non-polymers00
Water3,369187
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: KRAS peptide (VVVGAGGVGK)


Theoretical massNumber of molelcules
Total (without water)44,5773
Polymers44,5773
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-20 kcal/mol
Surface area19190 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: KRAS peptide (VVVGAGGVGK)


Theoretical massNumber of molelcules
Total (without water)44,5773
Polymers44,5773
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-20 kcal/mol
Surface area19260 Å2
MethodPISA
3
G: MHC class I antigen
H: Beta-2-microglobulin
I: KRAS peptide (VVVGAGGVGK)


Theoretical massNumber of molelcules
Total (without water)44,5773
Polymers44,5773
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-21 kcal/mol
Surface area19430 Å2
MethodPISA
4
J: MHC class I antigen
K: Beta-2-microglobulin
L: KRAS peptide (VVVGAGGVGK)


Theoretical massNumber of molelcules
Total (without water)44,5773
Polymers44,5773
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-21 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.854, 117.028, 110.643
Angle α, β, γ (deg.)90.00, 99.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22G
13A
23J
14B
24E
15B
25H
16B
26K
17D
27G
18D
28J
19E
29H
110E
210K
111G
211J
112H
212K

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLUAA2 - 2752 - 275
21SERSERGLUGLUDD2 - 2752 - 275
12SERSERGLUGLUAA2 - 2752 - 275
22SERSERGLUGLUGG2 - 2752 - 275
13SERSERTRPTRPAA2 - 2742 - 274
23SERSERTRPTRPJJ2 - 2742 - 274
14METMETMETMETBB0 - 991 - 100
24METMETMETMETEE0 - 991 - 100
15METMETMETMETBB0 - 991 - 100
25METMETMETMETHH0 - 991 - 100
16METMETMETMETBB0 - 991 - 100
26METMETMETMETKK0 - 991 - 100
17SERSERGLUGLUDD2 - 2752 - 275
27SERSERGLUGLUGG2 - 2752 - 275
18SERSERTRPTRPDD2 - 2742 - 274
28SERSERTRPTRPJJ2 - 2742 - 274
19METMETMETMETEE0 - 991 - 100
29METMETMETMETHH0 - 991 - 100
110METMETMETMETEE0 - 991 - 100
210METMETMETMETKK0 - 991 - 100
111SERSERTRPTRPGG2 - 2742 - 274
211SERSERTRPTRPJJ2 - 2742 - 274
112METMETMETMETHH0 - 991 - 100
212METMETMETMETKK0 - 991 - 100

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
MHC class I antigen


Mass: 31855.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A583ZB34
#2: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide
KRAS peptide (VVVGAGGVGK) / Transforming protein N-Ras / GTPase NRas


Mass: 843.003 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01111, small monomeric GTPase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.46→79.96 Å / Num. obs: 65854 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.074 / Rrim(I) all: 0.204 / Net I/σ(I): 9.3
Reflection shellResolution: 2.46→2.5 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.147 / Mean I/σ(I) obs: 2 / Num. unique obs: 3282 / CC1/2: 0.562 / Rpim(I) all: 0.44 / Rrim(I) all: 1.231 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HN7

2hn7


Resolution: 2.46→79.96 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.894 / SU B: 22.902 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.591 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25954 3237 4.9 %RANDOM
Rwork0.22804 ---
obs0.2296 62612 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å2-0 Å2-2.75 Å2
2--0.3 Å2-0 Å2
3----1.17 Å2
Refinement stepCycle: 1 / Resolution: 2.46→79.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12518 0 0 187 12705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01312860
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511498
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.65817444
X-RAY DIFFRACTIONr_angle_other_deg1.2441.58726470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.58551516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.74621.456824
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.026152108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.83115120
X-RAY DIFFRACTIONr_chiral_restr0.0750.21582
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214768
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023216
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_it0.7711.3926106
X-RAY DIFFRACTIONr_mcbond_other0.7711.3926105
X-RAY DIFFRACTIONr_mcangle_it1.3532.0867608
X-RAY DIFFRACTIONr_mcangle_other1.3532.0867609
X-RAY DIFFRACTIONr_scbond_it0.8521.486754
X-RAY DIFFRACTIONr_scbond_other0.8521.486754
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4652.1779836
X-RAY DIFFRACTIONr_long_range_B_refined2.92915.12413456
X-RAY DIFFRACTIONr_long_range_B_other2.92615.11513452
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A85920.08
12D85920.08
21A87590.07
22G87590.07
31A85700.08
32J85700.08
41B29880.07
42E29880.07
51B30500.06
52H30500.06
61B29960.07
62K29960.07
71D86180.08
72G86180.08
81D87060.06
82J87060.06
91E29760.08
92H29760.08
101E30240.07
102K30240.07
111G86010.07
112J86010.07
121H30080.06
122K30080.06
LS refinement shellResolution: 2.46→2.52 Å
RfactorNum. reflection% reflection
Rfree0.314 234 -
Rwork0.315 4582 -
obs--99.73 %
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)
11.1631-0.07-0.27591.5086-0.50592.2144-0.0274-0.036-0.10950.11160.04660.0940.0965-0.1032-0.01920.0196-0.01270.02990.0889-0.0520.2319-2.423620.0979-49.1949
22.2045-0.24310.50033.938-1.79222.9615-0.03280.02370.24130.1295-0.0133-0.2901-0.15680.09170.04620.0267-0.00230.01130.1574-0.04560.206211.05533.968-50.5514
30.5124-1.45631.5984.2803-4.70885.2008-0.1777-0.3014-0.12540.21590.70170.4008-0.1884-0.7883-0.5240.5510.2516-0.0450.468-0.10740.4865-7.644612.6284-32.1391
41.2923-0.06520.57621.2412-0.10971.3006-0.1329-0.10980.09990.07370.0864-0.0556-0.0292-0.03040.04650.18670.03040.05920.1845-0.06590.1504-28.265448.0202-17.9513
51.233-0.13371.77081.912-0.40975.1222-0.08210.0791-0.08790.02730.130.01640.1354-0.0605-0.0480.0938-0.00950.07370.141-0.00520.2201-36.320736.7682-31.4406
61.2029-0.71441.43840.4258-0.86071.7986-0.2584-0.00110.11730.1694-0.0014-0.0842-0.31380.12160.25980.32490.0084-0.02810.39320.00310.3524-12.401943.3258-9.597
71.85610.55730.42881.7960.4971.5261-0.04890.0740.0320.12170.1379-0.3674-0.19120.2036-0.0890.24940.01580.01610.14880.00240.2308-24.463983.1283-6.069
81.98571.39750.65813.93911.5163.05420.0025-0.0367-0.19510.62830.05520.04020.3603-0.0127-0.05770.27050.05930.01180.1873-0.0020.1867-33.871469.3163.8353
91.02121.84412.24695.41357.17559.6142-0.3035-0.1595-0.0885-0.29020.6926-0.3114-0.31291.1232-0.38910.52220.0787-0.04640.5086-0.01020.4753-8.796890.4070.0453
100.6821-0.00510.08141.136-0.04771.7169-0.04990.0060.0180.00440.08370.05810.10630.0808-0.03380.01390.00610.02230.17540.03990.2406-10.009655.3208-59.3177
111.90280.30262.04412.02720.74953.8951-0.07690.13330.0757-0.27240.11970.1509-0.1175-0.0508-0.04280.1057-0.03260.02820.15960.05760.2511-16.199966.2951-74.0043
120.00150.0020.00220.00310.00290.0039-0.0037-0.02020.01550.0073-0.03120.0197-0.004-0.02220.03490.273-0.018-0.00340.3888-0.04680.4291-13.030960.3367-41.1411
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 275
2X-RAY DIFFRACTION2B0 - 99
3X-RAY DIFFRACTION3C1 - 10
4X-RAY DIFFRACTION4D2 - 275
5X-RAY DIFFRACTION5E0 - 99
6X-RAY DIFFRACTION6F1 - 10
7X-RAY DIFFRACTION7G2 - 275
8X-RAY DIFFRACTION8H0 - 99
9X-RAY DIFFRACTION9I1 - 10
10X-RAY DIFFRACTION10J1 - 275
11X-RAY DIFFRACTION11K0 - 99
12X-RAY DIFFRACTION12L1 - 10

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  • 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

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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

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