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- PDB-2ak4: Crystal Structure of SB27 TCR in complex with HLA-B*3508-13mer peptide -

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Basic information

Entry
Database: PDB / ID: 2ak4
TitleCrystal Structure of SB27 TCR in complex with HLA-B*3508-13mer peptide
Components
  • (SB27 T cell receptor ...) x 2
  • Beta-2-microglobulinBeta-2 microglobulin
  • EBV peptide LPEPLPQGQLTAY
  • HLA-B35 variant
KeywordsIMMUNE SYSTEM / T cell receptor / bulged epitopes / pMHC-TCR complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / alpha-beta T cell receptor complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / alpha-beta T cell receptor complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / defense response / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / Downstream TCR signaling / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / T cell receptor signaling pathway / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / sequence-specific DNA binding / adaptive immune response / learning or memory / protein dimerization activity / immune response / Amyloid fiber formation / DNA-binding transcription factor activity / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / host cell nucleus
Similarity search - Function
Trans-activator protein BZLF1, human herpesvirus 4 / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / 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 ...Trans-activator protein BZLF1, human herpesvirus 4 / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / 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 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / : / T cell receptor alpha chain constant / T cell receptor beta constant 1 / HLA class I histocompatibility antigen, B alpha chain / Lytic switch protein BZLF1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTynan, F.E. / Burrows, S.R. / Buckle, A.M. / Clements, C.S. / Borg, N.A. / Miles, J.J. / Beddoe, T. / Whisstock, J.C. / Wilce, M.C. / Silins, S.L. ...Tynan, F.E. / Burrows, S.R. / Buckle, A.M. / Clements, C.S. / Borg, N.A. / Miles, J.J. / Beddoe, T. / Whisstock, J.C. / Wilce, M.C. / Silins, S.L. / Burrows, J.M. / Kjer-Nielsen, L. / Konstenko, L. / Purcell, A.W. / McCluskey, J. / Rossjohn, J.
CitationJournal: Nat.Immunol. / Year: 2005
Title: T cell receptor recognition of a 'super-bulged' major histocompatibility complex class I-bound peptide
Authors: Tynan, F.E. / Burrows, S.R. / Buckle, A.M. / Clements, C.S. / Borg, N.A. / Miles, J.J. / Beddoe, T. / Whisstock, J.C. / Wilce, M.C. / Silins, S.L. / Burrows, J.M. / Kjer-Nielsen, L. / ...Authors: Tynan, F.E. / Burrows, S.R. / Buckle, A.M. / Clements, C.S. / Borg, N.A. / Miles, J.J. / Beddoe, T. / Whisstock, J.C. / Wilce, M.C. / Silins, S.L. / Burrows, J.M. / Kjer-Nielsen, L. / Kostenko, L. / Purcell, A.W. / McCluskey, J. / Rossjohn, J.
History
DepositionAug 3, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA-B35 variant
B: Beta-2-microglobulin
C: EBV peptide LPEPLPQGQLTAY
D: SB27 T cell receptor alpha chain
E: SB27 T cell receptor beta chain
F: HLA-B35 variant
G: Beta-2-microglobulin
H: EBV peptide LPEPLPQGQLTAY
I: SB27 T cell receptor alpha chain
J: SB27 T cell receptor beta chain
K: HLA-B35 variant
L: Beta-2-microglobulin
M: EBV peptide LPEPLPQGQLTAY
N: SB27 T cell receptor alpha chain
P: SB27 T cell receptor beta chain
Q: HLA-B35 variant
R: Beta-2-microglobulin
S: EBV peptide LPEPLPQGQLTAY
T: SB27 T cell receptor alpha chain
U: SB27 T cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)390,02942
Polymers387,23720
Non-polymers2,79222
Water4,306239
1
A: HLA-B35 variant
B: Beta-2-microglobulin
C: EBV peptide LPEPLPQGQLTAY
D: SB27 T cell receptor alpha chain
E: SB27 T cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,69812
Polymers96,8095
Non-polymers8887
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA-B35 variant
G: Beta-2-microglobulin
H: EBV peptide LPEPLPQGQLTAY
I: SB27 T cell receptor alpha chain
J: SB27 T cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,69812
Polymers96,8095
Non-polymers8887
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: HLA-B35 variant
L: Beta-2-microglobulin
M: EBV peptide LPEPLPQGQLTAY
N: SB27 T cell receptor alpha chain
P: SB27 T cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3179
Polymers96,8095
Non-polymers5084
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
Q: HLA-B35 variant
R: Beta-2-microglobulin
S: EBV peptide LPEPLPQGQLTAY
T: SB27 T cell receptor alpha chain
U: SB27 T cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3179
Polymers96,8095
Non-polymers5084
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.154, 213.282, 122.303
Angle α, β, γ (deg.)90.00, 89.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
31K
41Q
51A
61F
71K
81Q
91A
101F
111K
121Q
131A
141F
151K
161Q
171A
181F
191K
201Q
12B
22G
32L
42R
13D
23I
33N
43T
53D
63I
73N
83T
93D
103I
113N
123T
133D
143I
153N
163T
173D
183I
193N
203T
14D
24I
34N
44T
54D
64I
74N
84T
94D
104I
114N
124T
15E
25J
35P
45U
55E
65J
75P
85U
95E
105J
115P
125U
135E
145J
155P
165U
16C
26H
36M
46S
17E
27J
37P
47U
57E
67J
77P
87U
97E
107J
117P
127U

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111HISALAAA3 - 403 - 40
211HISALAFF3 - 403 - 40
311HISALAKK3 - 403 - 40
411HISALAQP3 - 403 - 40
521PROCYSAA43 - 10143 - 101
621PROCYSFF43 - 10143 - 101
721PROCYSKK43 - 10143 - 101
821PROCYSQP43 - 10143 - 101
931ARGGLNAA111 - 144111 - 144
1031ARGGLNFF111 - 144111 - 144
1131ARGGLNKK111 - 144111 - 144
1231ARGGLNQP111 - 144111 - 144
1341LYSHISAA146 - 192146 - 192
1441LYSHISFF146 - 192146 - 192
1541LYSHISKK146 - 192146 - 192
1641LYSHISQP146 - 192146 - 192
1751GLUGLYAA198 - 265198 - 265
1851GLUGLYFF198 - 265198 - 265
1951GLUGLYKK198 - 265198 - 265
2051GLUGLYQP198 - 265198 - 265
112ILEMETBB1 - 991 - 99
212ILEMETGG1 - 991 - 99
312ILEMETLL1 - 991 - 99
412ILEMETRQ1 - 991 - 99
113GLNVALDD1 - 234 - 26
213GLNVALII1 - 234 - 26
313GLNVALNN1 - 234 - 26
413GLNVALTS1 - 234 - 26
523LEUARGDD32 - 4836 - 52
623LEUARGII32 - 4836 - 52
723LEUARGNN32 - 4836 - 52
823LEUARGTS32 - 4836 - 52
933ARGLEUDD61 - 9265 - 96
1033ARGLEUII61 - 9265 - 96
1133ARGLEUNN61 - 9265 - 96
1233ARGLEUTS61 - 9265 - 96
1343ILETHRDD105 - 110106 - 111
1443ILETHRII105 - 110106 - 111
1543ILETHRNN105 - 110106 - 111
1643ILETHRTS105 - 110106 - 111
1753LEUPRODD112 - 116113 - 117
1853LEUPROII112 - 116113 - 117
1953LEUPRONN112 - 116113 - 117
2053LEUPROTS112 - 116113 - 117
114ASNGLNDD117 - 127118 - 128
214ASNGLNII117 - 127118 - 128
314ASNGLNNN117 - 127118 - 128
414ASNGLNTS117 - 127118 - 128
524CYSASPDD139 - 155140 - 156
624CYSASPII139 - 155140 - 156
724CYSASPNN139 - 155140 - 156
824CYSASPTS139 - 155140 - 156
934VALSERDD158 - 206159 - 207
1034VALSERII158 - 206159 - 207
1134VALSERNN158 - 206159 - 207
1234VALSERTS158 - 206159 - 207
115GLYALAEE3 - 245 - 26
215GLYALAJJ3 - 245 - 26
315GLYALAPO3 - 245 - 26
415GLYALAUT3 - 245 - 26
525TYRTYREE33 - 4835 - 50
625TYRTYRJJ33 - 4835 - 50
725TYRTYRPO33 - 4835 - 50
825TYRTYRUT33 - 4835 - 50
935THRSEREE55 - 9457 - 95
1035THRSERJJ55 - 9457 - 95
1135THRSERPO55 - 9457 - 95
1235THRSERUT55 - 9457 - 95
1345PHEVALEE108 - 116106 - 114
1445PHEVALJJ108 - 116106 - 114
1545PHEVALPO108 - 116106 - 114
1645PHEVALUT108 - 116106 - 114
116LEUTYRCC1 - 131 - 13
216LEUTYRHH1 - 131 - 13
316LEUTYRMM1 - 131 - 13
416LEUTYRSR1 - 131 - 13
117THRTHREE117 - 227115 - 225
217THRTHRJJ117 - 227115 - 225
317THRTHRPO117 - 227115 - 225
417THRTHRUT117 - 227115 - 225
527ARGGLUEE230 - 241228 - 239
627ARGGLUJJ230 - 241228 - 239
727ARGGLUPO230 - 241228 - 239
827ARGGLUUT230 - 241228 - 239
937GLYASPEE244 - 247242 - 245
1037GLYASPJJ244 - 247242 - 245
1137GLYASPPO244 - 247242 - 245
1237GLYASPUT244 - 247242 - 245

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

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Protein , 2 types, 8 molecules AFKQBGLR

#1: Protein
HLA-B35 variant


Mass: 31984.281 Da / Num. of mol.: 4 / Fragment: Extracellular domains, alpha1,2,3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET 30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 297143, UniProt: P01889*PLUS
#2: Protein
Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P61769

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Protein/peptide , 1 types, 4 molecules CHMS

#3: Protein/peptide
EBV peptide LPEPLPQGQLTAY


Mass: 1426.612 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthetic peptide LPEPLPQGQLTAY / References: UniProt: P03206*PLUS

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SB27 T cell receptor ... , 2 types, 8 molecules DINTEJPU

#4: Protein
SB27 T cell receptor alpha chain


Mass: 24006.436 Da / Num. of mol.: 4 / Fragment: Extracellular Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P01848*PLUS
#5: Protein
SB27 T cell receptor beta chain


Mass: 27643.723 Da / Num. of mol.: 4 / Fragment: Extracellular Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P01850*PLUS

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Non-polymers , 2 types, 261 molecules

#6: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: I
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 200mM Potassium Iodide, 16% PEG 3350, 100mM Na Cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 134769 / Net I/σ(I): 12.98
Reflection shellHighest resolution: 2.5 Å / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.866 / SU B: 25.35 / SU ML: 0.269 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.681 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 4033 3 %RANDOM
Rwork0.246 ---
all0.247 ---
obs0.247 133366 95.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.386 Å2
Baniso -1Baniso -2Baniso -3
1--3.06 Å20 Å20.24 Å2
2--5.54 Å20 Å2
3----2.48 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26348 0 22 239 26609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02127098
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.93236933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.36853308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90323.7181361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.331154097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.73215192
X-RAY DIFFRACTIONr_chiral_restr0.0680.23896
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0221416
X-RAY DIFFRACTIONr_nbd_refined0.1810.210176
X-RAY DIFFRACTIONr_nbtor_refined0.30.217996
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2935
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.2116
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.213
X-RAY DIFFRACTIONr_mcbond_it0.841316702
X-RAY DIFFRACTIONr_mcangle_it1.606526798
X-RAY DIFFRACTIONr_scbond_it2.413711699
X-RAY DIFFRACTIONr_scangle_it3.9921010135
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberRmsTypeWeight
11A19810.02TIGHT POSITIONAL0.05
12F19810.02TIGHT POSITIONAL0.05
13K19810.03TIGHT POSITIONAL0.05
14Q19810.02TIGHT POSITIONAL0.05
11A19810.05TIGHT THERMAL0.5
12F19810.05TIGHT THERMAL0.5
13K19810.05TIGHT THERMAL0.5
14Q19810.05TIGHT THERMAL0.5
21B7750.02TIGHT POSITIONAL0.05
22G7750.02TIGHT POSITIONAL0.05
23L7750.02TIGHT POSITIONAL0.05
24R7750.02TIGHT POSITIONAL0.05
21B7750.04TIGHT THERMAL0.5
22G7750.04TIGHT THERMAL0.5
23L7750.04TIGHT THERMAL0.5
24R7750.04TIGHT THERMAL0.5
31D6580.02TIGHT POSITIONAL0.05
32I6580.02TIGHT POSITIONAL0.05
33N6580.02TIGHT POSITIONAL0.05
34T6580.03TIGHT POSITIONAL0.05
31D6580.04TIGHT THERMAL0.5
32I6580.04TIGHT THERMAL0.5
33N6580.05TIGHT THERMAL0.5
34T6580.05TIGHT THERMAL0.5
41D5520.01TIGHT POSITIONAL0.05
42I5520.01TIGHT POSITIONAL0.05
43N5520.02TIGHT POSITIONAL0.05
44T5520.02TIGHT POSITIONAL0.05
41D5520.03TIGHT THERMAL0.5
42I5520.02TIGHT THERMAL0.5
43N5520.03TIGHT THERMAL0.5
44T5520.02TIGHT THERMAL0.5
51E6660.02TIGHT POSITIONAL0.05
52J6660.02TIGHT POSITIONAL0.05
53P6660.04TIGHT POSITIONAL0.05
54U6660.02TIGHT POSITIONAL0.05
51E6660.04TIGHT THERMAL0.5
52J6660.04TIGHT THERMAL0.5
53P6660.05TIGHT THERMAL0.5
54U6660.04TIGHT THERMAL0.5
61C960.02TIGHT POSITIONAL0.05
62H960.02TIGHT POSITIONAL0.05
63M960.03TIGHT POSITIONAL0.05
64S960.02TIGHT POSITIONAL0.05
61C960.04TIGHT THERMAL0.5
62H960.05TIGHT THERMAL0.5
63M960.04TIGHT THERMAL0.5
64S960.04TIGHT THERMAL0.5
71E9570.02TIGHT POSITIONAL0.05
72J9570.02TIGHT POSITIONAL0.05
73P9570.02TIGHT POSITIONAL0.05
74U9570.02TIGHT POSITIONAL0.05
71E9570.04TIGHT THERMAL0.5
72J9570.04TIGHT THERMAL0.5
73P9570.04TIGHT THERMAL0.5
74U9570.03TIGHT THERMAL0.5
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 293 -
Rwork0.32 9778 -
all-10071 -
obs--97.55 %

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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

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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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