[English] 日本語
Yorodumi
- PDB-7ux5: Structure of PDL1 in complex with FP28136, a Helicon Polypeptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ux5
TitleStructure of PDL1 in complex with FP28136, a Helicon Polypeptide
Components
  • Helicon FP28136
  • Programmed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / Complex / stapled
Function / homology
Function and homology information


positive regulation of tolerance induction to tumor cell / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production ...positive regulation of tolerance induction to tumor cell / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of type II interferon production / PD-1 signaling / positive regulation of T cell proliferation / T cell costimulation / response to cytokine / recycling endosome membrane / actin cytoskeleton / early endosome membrane / cellular response to lipopolysaccharide / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / positive regulation of cell migration / immune response / external side of plasma membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
N,N'-(1,4-phenylene)diacetamide / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsAgarwal, S. / Li, K. / Tokareva, O. / Thomson, T. / Travaline, T. / Wahl, S. / Verdine, G. / McGee, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: De novo mapping of alpha-helix recognition sites on protein surfaces using unbiased libraries.
Authors: Li, K. / Tokareva, O.S. / Thomson, T.M. / Wahl, S.C.T. / Travaline, T.L. / Ramirez, J.D. / Choudary, S.K. / Agarwal, S. / Walkup 4th, W.G. / Olsen, T.J. / Brennan, M.J. / Verdine, G.L. / McGee, J.H.
History
DepositionMay 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Programmed cell death 1 ligand 1
C: Programmed cell death 1 ligand 1
B: Helicon FP28136
D: Helicon FP28136
E: Programmed cell death 1 ligand 1
F: Helicon FP28136
G: Programmed cell death 1 ligand 1
H: Helicon FP28136
I: Programmed cell death 1 ligand 1
J: Helicon FP28136
K: Programmed cell death 1 ligand 1
L: Helicon FP28136
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,40518
Polymers101,25212
Non-polymers1,1536
Water00
1
A: Programmed cell death 1 ligand 1
B: Helicon FP28136
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0673
Polymers16,8752
Non-polymers1921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Programmed cell death 1 ligand 1
D: Helicon FP28136
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0673
Polymers16,8752
Non-polymers1921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Programmed cell death 1 ligand 1
F: Helicon FP28136
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0673
Polymers16,8752
Non-polymers1921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Programmed cell death 1 ligand 1
H: Helicon FP28136
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0673
Polymers16,8752
Non-polymers1921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Programmed cell death 1 ligand 1
J: Helicon FP28136
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0673
Polymers16,8752
Non-polymers1921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Programmed cell death 1 ligand 1
L: Helicon FP28136
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0673
Polymers16,8752
Non-polymers1921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.477, 77.882, 127.747
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 18 through 44 or resid 48...
d_2ens_1(chain "C" and (resid 18 through 44 or resid 48...
d_3ens_1(chain "E" and (resid 18 through 44 or resid 48...
d_4ens_1(chain "G" and (resid 18 through 44 or resid 48...
d_5ens_1(chain "I" and (resid 18 through 44 or resid 48...
d_6ens_1(chain "K" and (resid 18 through 70 or resid 72...
d_1ens_2(chain "B" and (resid 1 through 16 or resid 101))
d_2ens_2(chain "D" and (resid 1 through 16 or resid 101))
d_3ens_2(chain "F" and (resid 1 through 16 or resid 101))
d_4ens_2(chain "H" and (resid 1 through 16 or resid 101))
d_5ens_2(chain "J" and (resid 1 through 16 or resid 101))
d_6ens_2(chain "L" and (resid 1 through 16 or resid 101))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAVALA1 - 27
d_12ens_1LEUGLYA31 - 53
d_13ens_1GLULEUA55 - 57
d_14ens_1VALLYSA59 - 72
d_15ens_1GLNASNA74 - 114
d_21ens_1ALAVALB1 - 27
d_22ens_1LEUGLYB31 - 53
d_23ens_1GLULEUB55 - 57
d_24ens_1VALLYSB59 - 72
d_25ens_1GLNASNB74 - 114
d_31ens_1ALAVALG1 - 27
d_32ens_1LEUGLYG31 - 53
d_33ens_1GLULEUG55 - 57
d_34ens_1VALLYSG59 - 72
d_35ens_1GLNASNG74 - 114
d_41ens_1ALAVALJ1 - 27
d_42ens_1LEUGLYJ31 - 53
d_43ens_1GLULEUJ55 - 57
d_44ens_1VALLYSJ59 - 72
d_45ens_1GLNASNJ74 - 114
d_51ens_1ALAVALM1 - 27
d_52ens_1LEUGLYM31 - 53
d_53ens_1GLULEUM55 - 57
d_54ens_1VALLYSM59 - 72
d_55ens_1GLNASNM74 - 114
d_61ens_1ALAGLYP1 - 50
d_62ens_1GLULEUP52 - 54
d_63ens_1VALLYSP56 - 69
d_64ens_1GLNASNP71 - 111
d_11ens_2ASPGLUC1 - 16
d_12ens_2WHLWHLD
d_21ens_2ASPGLUE1 - 16
d_22ens_2WHLWHLF
d_31ens_2ASPGLUH1 - 16
d_32ens_2WHLWHLI
d_41ens_2ASPGLUK1 - 16
d_42ens_2WHLWHLL
d_51ens_2ASPGLUN1 - 16
d_52ens_2WHLWHLO
d_61ens_2ASPGLUQ1 - 16
d_62ens_2WHLWHLR

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.375700324402, 0.179660712287, -0.909159664033), (0.196239672495, -0.974205036856, -0.111420541655), (-0.905725817885, -0.136552461071, -0.40126570772)-15.1273950397, -9.41534241741, -25.3657835081
2given(-0.534470599955, -0.281758083762, -0.796839732957), (-0.453172211049, -0.700284483516, 0.551576458235), (-0.713425626759, 0.65590702419, 0.246596534245)22.9465706958, -8.71977870723, -28.0436376011
3given(0.584561943154, -0.34618883027, 0.73378513777), (0.263768024292, -0.77418765244, -0.575378056734), (0.767276849629, 0.529893170937, -0.361247094684)7.20329250665, -13.6514894891, -69.9731882209
4given(-0.436514163763, -0.289777353043, -0.851753761657), (-0.778186940852, 0.596731838927, 0.195796316358), (0.451531250216, 0.748291519446, -0.485982851553)22.2323658635, 29.0514059448, -34.4519483454
5given(0.51252990679, -0.377657539518, 0.771160085515), (0.460041635369, 0.879088632294, 0.124759249348), (-0.725034335996, 0.290822900432, 0.624297406859)16.6899558268, -33.6711912412, 13.9680539479
6given(0.535018293854, 0.295809596174, 0.791360921485), (-0.362984365531, -0.765349544388, 0.531490757479), (0.762887787045, -0.571608920257, -0.302101748855)54.8526537699, 29.2326356197, -34.1216924057
7given(-0.795853482844, 0.501604876966, -0.339130920514), (0.433923202054, 0.0818637461227, -0.897222927588), (-0.422288868625, -0.861214766754, -0.282809541849)12.1162021965, -73.0929076656, -56.0805002319
8given(-0.528730283442, 0.461642169892, 0.712271573453), (0.361036017528, 0.881781528898, -0.303503425586), (-0.768177896986, 0.0966842400423, -0.632894048249)44.6112217222, -21.5236936391, -62.6448765548
9given(-0.796930785293, 0.568365726268, -0.204601379899), (-0.470613760392, -0.796513856648, -0.379589732074), (-0.378713627933, -0.206218518496, 0.902247144993)21.5586250371, -4.37212752112, 28.9740630099
10given(0.996468947605, -0.03730409518, -0.0752199504177), (0.0354393302906, -0.625294645743, 0.779583645207), (-0.0761162947508, -0.779496639177, -0.621764665437)4.00612335215, 11.8022532442, -39.6791758266

-
Components

#1: Protein
Programmed cell death 1 ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 14809.955 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7
#2: Protein/peptide
Helicon FP28136


Mass: 2065.307 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.43 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS pH 8, 25% v/v PEG 350 MME.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 3.35→49.02 Å / Num. obs: 11440 / % possible obs: 99.64 % / Redundancy: 10.8 % / Biso Wilson estimate: 84.48 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.199 / Net I/σ(I): 9.9
Reflection shellResolution: 3.35→3.47 Å / Rmerge(I) obs: 0.75 / Num. unique obs: 25562 / CC1/2: 0.949

-
Processing

Software
NameVersionClassification
PHENIX1.20_4444refinement
XSCALEdata scaling
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C3T

5c3t


Resolution: 3.35→49.02 Å / SU ML: 0.511 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.5823
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3007 550 4.81 %
Rwork0.2332 10887 -
obs0.2365 11437 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.62 Å2
Refinement stepCycle: LAST / Resolution: 3.35→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6417 0 84 0 6501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00586627
X-RAY DIFFRACTIONf_angle_d1.04578961
X-RAY DIFFRACTIONf_chiral_restr0.0619981
X-RAY DIFFRACTIONf_plane_restr0.00631135
X-RAY DIFFRACTIONf_dihedral_angle_d16.83942413
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.400500517692
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.478242121953
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.392318831841
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.481185632814
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.444302257466
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.218465458371
ens_2d_3CX-RAY DIFFRACTIONTorsion NCS0.216905558896
ens_2d_4CX-RAY DIFFRACTIONTorsion NCS0.215707317337
ens_2d_5CX-RAY DIFFRACTIONTorsion NCS0.210308759941
ens_2d_6CX-RAY DIFFRACTIONTorsion NCS0.206678679007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.690.36151150.28412667X-RAY DIFFRACTION99.53
3.69-4.220.31831740.25662654X-RAY DIFFRACTION99.96
4.22-5.310.28081180.20882734X-RAY DIFFRACTION99.79
5.32-49.020.28251430.21992832X-RAY DIFFRACTION99.37
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)
17.91563065838-3.328713116310.2794459699159.44875074090.7095719511438.456185679680.651082122382-0.242582896153-1.426941314220.12119834348-0.410188906146-0.64612803562-0.008071312894940.82436973816-0.1947309141570.309864760006-0.0676211719687-0.0708197589370.7428887715230.008101302103380.85269968078918.97526826871.47543734953-14.5170028744
24.03011865628-1.109464618681.576349309732.510520931263.225284302836.51620339181-0.467683032015-0.787822308642-0.2362171492060.525277492268-0.641380608871.49358806912-0.6408787453531.151496317151.105012693730.772998032018-0.0576031575680.170818976270.836269728564-0.1160244330630.5367596349289.5734774905218.0339196661-5.27576846075
37.844657696250.9610982493842.949605937789.26824278756-1.966337953815.444396656710.217099725205-0.89524644401-0.6514059317191.020647177530.02680655677250.51231535037-0.726207876568-0.117569205753-0.186617703330.6194422711430.08123877624450.04055893187110.5593567668570.09403068638820.3983658458875.02847472724-0.511580765734-6.76897110915
42.044762201297.019411188757.695477178532.006549729169.909734130737.735443280990.915566455334-1.863276353060.3250435577382.46060421159-0.006684726111081.563893248454.58346901951-0.523145444826-0.7053435781621.11800317030.2068093206520.1401096882291.096303640230.1836399321980.67753831249810.6780723433-10.3651821374-3.9079727242
57.168841818722.01351687637-0.02651265990252.03668978457-6.795553424883.63083912321.89150208806-0.8104523821970.219570503188-0.189615612827-2.681753371072.36975396980.5859954138240.5198995304720.9036021584670.6206730910830.0861625131167-0.1876410931190.64181445944-0.0698147667730.67782178497115.56761729696.50175647858-2.72658069086
66.0447547638-6.92455661234-2.93716441412.02445271654.033570814471.28471487143-1.36144512555-0.571864117362-0.7414219449231.606682030441.75510477380.0118583683290.8351322933680.144747027027-0.5228627107520.6613368687020.228491821914-0.2427916205131.056346961420.025486573750.85087265882817.2127374077-5.84640646357-9.11309705374
78.96509726606-3.58931749784-1.166914000067.240501575731.907506181554.2453892105-0.609011494532-0.683676043845-1.34948492657-0.1347489485990.429824310590.1155560378930.2801537803771.143337581010.1310069173150.3410408198610.02695041667890.09773161266130.6811766202530.0005178470630070.59660507576412.00300849421.07599254742-16.3725510366
83.968983367943.634387259761.013632680957.03414714958-2.80144829288.01047302609-1.0859728880.265576270726-0.0244412371356-0.4542011130390.932737450399-1.76437979097-0.0660460785720.3688048948980.1524762881460.507566458950.00383402207440.07491057291310.5802802625940.003522733353090.6627027942125.47358282399-5.46615191077-36.9440554296
92.032563928423.00053659962-3.504523008092.88514404711-3.518978382017.18687046401-0.2025369846780.359464711847-2.62715623175-2.51572387777-0.663569793951-0.6597828074272.536119428431.140537866340.8609966392772.016617677430.065531109829-0.5572656212350.8130134823750.2425259153541.33683385225-3.86973777784-24.1208000416-34.697474546
106.892279153354.64261892663-5.367349134247.994148725741.770985316636.360859549360.02415281629540.2192905972220.0675081822837-0.963969567863-0.2853499164081.25558362587-0.0769820989763-0.9749729108630.3474368412210.6651451429990.0110674239285-0.2562595043540.7211164291770.0412499425530.746618779885-7.26930437654-6.67239638167-30.5634416339
118.033675324431.599861101493.121410160182.16652017939-7.945791252728.25327141393-1.034200655880.005648420965591.02009914335-0.6901586593850.6757739228190.2024800146670.0337653936141-0.939388273210.2319249783310.7254522673240.0307338600728-0.1218700369260.6040712562620.009526738392310.656545529199-0.249459647275-4.18580761865-32.7877912666
122.65419685928-2.34414061845-0.8115053705099.16641211329-2.421650513219.79056993031-0.06776944783020.09730225089220.5876014218212.0774838252-0.0253226332662-0.964418450609-0.841085187296-0.1859193430910.1723948777040.417886183472-0.058885285988-0.1072996921530.54585387053-0.09092805198120.5544015222157.37500391118-1.10781552769-32.313051895
139.282050570737.998614362840.4976204504269.19456752102-3.068678393769.545713318150.750617021224-1.184366052750.1352114313950.751344319048-0.1916271270190.383302670570.06248808206410.187575305349-0.5810998539620.3822598507350.03170225860190.06518476850150.686844986773-0.03239485600690.448065366008-2.33051680402-3.41747844634-10.2955182596
145.98332287456-2.817991139465.157288422888.68118147181-5.240780630812.58550399207-0.482423927034-0.839568476169-0.0374612634147-1.026766222691.433179984790.6022390436020.247771133574-1.33862279021-0.7840797571120.6780292534550.0511307242502-0.01942233152820.624865124417-0.05662509274320.604462180871-7.38490802955-5.52045897872-18.5164563805
154.245541636352.00401723287-2.367916873416.67264227969-0.4968585543474.60030231747-0.0681597219697-0.00810035151001-0.03721603540440.286394276956-0.09532791608050.980671204094-0.000353116376201-1.058847469130.1252770339610.4955326777270.01503012905190.03600823065850.966208081114-0.03427640589730.80655688678823.0825193939-20.1730788135-37.726800332
164.187364580940.855828341568-1.796818609963.341228419330.04717122091265.79419832784-0.01796560886450.333508084129-0.135458900727-0.3729962133890.3631832869630.458658921581-0.1653582661471.10446665093-0.3755895596250.712250840849-0.03716395190820.1291337037560.621551109553-0.1176294175860.79037496132728.9715658754-24.3652568617-46.3110507062
175.267742305533.06823338467-1.782882587253.81263629557-2.719936283968.047598911130.844810420598-0.8218320377210.7995200027470.262545606959-0.7899522971930.626559653288-1.01989783432-1.07341463191-0.2816542937850.9013154614760.1032582174540.05972443139611.32015335843-0.3712640812490.83288883502633.5353459102-11.1103914139-31.1659023715
187.744408830526.82922560927.30146062881.997820987768.139045020047.097274160410.737669654668-1.53732726768-0.2682709154250.806438636629-1.067650451980.310450998-0.18207573245-0.5518792083630.4098543074710.693690316521-0.274844666490.2079516632220.728875569707-0.09508515214830.639521451149-0.86062534903-7.09102789701-47.1718586899
196.892717667571.97066839101-2.31351935767.25023930684-3.952156468612.11112663031-1.560478594920.604894223917-0.545283406908-0.02387178335190.263416926435-1.33393376741-2.327030768782.242201116331.212305516271.02976306476-0.319499783361-0.1311865396261.361360161890.2552020519561.0316322136313.86033347766.11486933375-50.9742204187
200.433378201963-0.5368011173861.516507083627.365259906720.3386222487154.86977541923-0.38603018161-0.695226428779-0.1499859992270.4320187487620.356627968436-0.8625313422870.1073839209810.4878876114090.02074589565490.3554584258150.0597410289907-0.1230086329590.9187404750640.100041665930.878107058495.0227699206-15.4683259416-50.6669334654
219.277276454960.606277330513.186588471789.070404630172.192860528929.603572199340.09208830438332.1224267850.404651489838-0.6485709341320.0785870084796-0.260319439708-0.7104236247291.48811919385-0.07576400796660.455996711472-0.09918427099150.09680130134010.7443315247620.02796209637150.5260328273163.69342217906-6.21865756125-62.0133467877
225.13150490197-2.675502972221.584845099762.09344515002-8.687516896436.184916274160.8303722883681.51459081693-0.745837449021-0.0223298959443-2.08569349726-0.17711474064-0.2878057623330.9999081106741.327931088430.8662374087710.04575362975320.05208546892360.926344832506-0.07233048272450.7216591327458.50147547048-10.9328218362-67.1387667658
231.92411983146-3.501545687810.5291202607136.71893579914-2.173637868147.56434669209-0.999033257330.210028186547-0.741258644537-0.2956388353290.228563365309-4.970691913371.06375437547-1.370155887690.5522317700031.12834339189-0.442438240736-0.1434543212311.224237284280.7248543954412.3100998043313.70167141-0.922808195432-65.5571079116
240.545363434083-0.7683980857942.075645346352.121360411382.356825541381.955029562470.327038092369-1.399919891911.159626859110.4072101423580.205013255943-3.816896869750.215678539333.77536279079-0.3063682277710.6196821169550.202167604071-0.01137313152591.081276873330.2181503512081.5720634457512.0901010833-12.9043008545-53.7726510072
258.03910511387-1.439568142663.299152892119.229216649322.463792975077.489611837421.477198311740.545357972632.032986373730.6217232914370.130507233742-0.362170155624-0.9705486347031.52261065569-1.71889707720.723647193151-0.04188154708240.06661672203790.547503501876-0.1074593727241.2303822884210.5766603137-7.00130224871-53.2377545447
263.143329137982.52784986901-2.608621377893.139896813270.2212433196057.34239787471.55030894519-0.352923360957-1.85292261874-1.5745482951-0.444939373044-0.313776876241-1.034654458491.32740782615-0.7225403897231.0594152164-0.527483159576-0.2638341163071.082027669921.416318233862.0916536931414.16910822286.45950546431-59.0609622154
279.30285660984-3.541117096752.962854216626.57828926944.293755218166.05691117548-0.5645240892271.396113390450.422958600117-0.7903828266470.6986306703660.814244611128-0.5273685321960.609966238398-0.1204416702160.573814444134-0.1303348819560.01078107008480.4198951469410.0701653733080.4149168687490.678721622443-2.99612964162-54.46198493
286.202826878883.98353915815-7.175171079126.09897436585-7.042848188212.26955665356-0.3107083305920.174182305939-0.123036860968-0.08148645068430.236463810578-0.3987688905720.8163873620640.5532511207280.2237209307760.816658114003-0.1256445476220.05762441052570.674054201916-0.05847751099710.493123872837-0.628636568569-5.66337203713-69.916774505
298.548705253113.880430475-3.464007591068.6740732673-4.021493547432.001303479510.07444191549730.0741492865685-0.9236100303430.801511394346-0.2431011158-0.829977099984-0.132183831983-0.1463522564840.11154400490.6771449135040.04290829290940.002594919952521.15562184870.1465594452170.60276521145725.892838409512.2730603685-17.7583991018
304.969710360822.193848274740.813296391892.929198917690.7727180627930.1416392258620.850613457627-1.18016710028-0.143182988008-0.2313691111240.417422075461-1.88047695496-1.69783469615-0.633175271611-0.8388756438110.8488718093310.3126508274990.3056138459141.38986626256-0.002335980625230.89304475159117.07717189230.6471801439-14.2081922637
315.26313366715-4.01854066449-3.884797072788.80500645536-0.1162915106545.313105411480.1586812184690.3958088726770.256142080635-1.206544812150.391899545080.2819150108530.0907777853044-0.260473200366-0.511889774370.674283894027-0.179280444376-0.1320015359110.9515380853880.02821990962860.6993749564627.968473663722.2885721874-27.2065649423
327.8303646369-0.32833019772-1.479087559047.84722119397-5.153220070564.01623869976-0.04944729973240.9482796522090.151425080306-0.6072800570060.9960938441780.253202902943-0.135695623982-1.87125770311-0.9412060039110.776245333853-0.03753012816-0.2680566250251.150792147470.07571834739330.79784522694622.941559576620.6707566147-33.9941051912
339.490703670351.53424926084-5.815773615187.515028461472.712280137052.0883849850.6906391065110.5894109019660.0682081183711-0.2329237301360.1655037102111.05705780988-0.132669673989-2.58796473215-0.8253291738330.486343544931-0.094235277806-0.03184523239540.8064826499940.1607054884950.87443938114717.64014732718.8682999552-21.4156829403
349.270090746423.09192657118-1.593131695974.436870274891.625831268848.176880094060.0848634564942-0.204461105362-0.1786582885060.212468444105-0.610047622328-0.2602668109230.950041901808-0.02676296325560.4454539971260.6017032080810.08687047375130.2188261982770.5905039673940.1732183708460.73570212529629.832957263214.3357451886-22.834491581
355.680738408323.816080333313.407860809662.558820757692.965191474062.14227605033-0.90890129941-0.395648869328-0.637606426771-0.755487062852-0.004363464817240.364163763349-0.914671210495-0.8714563955690.9288398078440.8071852567330.1611582576240.09556509116140.7710726374170.3362951514651.2479582545533.105571140126.9940376384-32.6689414427
366.20711053361-0.977737714529-1.789308986362.760691255864.253204419085.389106225610.183598096380.7768890776720.616817682782-0.589575620432-0.160006575242-0.725361079914-0.6759509780720.211537297495-0.1066964461710.866668017957-0.0970916805645-0.02851197070140.7111828514950.2214149717650.7689573668114.7546140178-25.4571318549-8.52574273432
372.001312892418.187138073562.956578207852.01207176609-4.144967026696.773207556082.4043661285-2.994346219733.131392574270.615998102344-0.6673950403782.38572717860.582879056284.27761468342-1.652161038760.748559020826-0.05031490961890.09487149981562.18373178784-0.09724682792491.043192319110.9094148507-16.84223457318.95921608076
381.91390944663-8.8383113556-5.554137447329.657212559591.940814975085.692756825730.4176831816870.4363090888040.5720171716380.644786117236-2.38413286389-0.553152455912-0.456751333042-1.549026032112.014778689060.654466628263-0.105200626097-0.1320051439180.836743490676-0.1824872535680.95448365736912.392988177-32.39292064223.44119482246
399.962749192610.7463950474524.508935406637.85127426617-5.324925383096.11072275359-1.413485203480.8580602516042.058520142011.33392354649-1.983601752170.837650251089-4.400499405752.224920708312.950944528911.4150138289-0.275106013306-0.384770403441.046203443710.07180265736031.1943777406117.4671480518-33.35957986310.0337254743
400.689787605337-3.179829979910.05273727758452.0770814417-1.189311449355.62008803077-0.4577054050690.370052890976-0.07308298527830.4778961032090.349395023011-2.51786137319-0.5716652666440.7706948705880.1805809016350.643350611754-0.2675086290520.06003781811441.07601350878-0.1365884101491.0847065947920.5778168685-27.3118490341.01766992361
416.25726054794-1.20458642605-5.385297361454.182767034510.4288722760297.250568317320.13175771102-0.164911821055-0.03925976312950.4898723006640.227160253188-0.661337690822-0.2477369626490.437918674956-0.5529899989770.548311425141-0.247802448278-0.04106033326710.680433091734-0.05864939175430.62351087893612.8901076986-31.3418380803-5.72046221567
422.27029870081-5.641729685282.246947187588.76562581315-4.365953117116.85278893492-0.566550265384-2.564521053280.1929608135280.830034011520.824677807144-0.720765876667-1.586357646710.851374863502-0.2471356983990.981913563238-0.2571938765310.1310704838521.0894579928-0.08710565222810.7344845750638.81867587435-39.19081306788.2530688356
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 18 through 41 )AA18 - 411 - 24
22chain 'A' and (resid 42 through 52 )AA42 - 5225 - 35
33chain 'A' and (resid 53 through 78 )AA53 - 7836 - 61
44chain 'A' and (resid 79 through 84 )AA79 - 8462 - 67
55chain 'A' and (resid 85 through 94 )AA85 - 9468 - 77
66chain 'A' and (resid 95 through 109 )AA95 - 10978 - 92
77chain 'A' and (resid 110 through 133 )AA110 - 13393 - 116
88chain 'C' and (resid 18 through 41 )CB18 - 411 - 24
99chain 'C' and (resid 42 through 52 )CB42 - 5225 - 35
1010chain 'C' and (resid 53 through 94 )CB53 - 9436 - 77
1111chain 'C' and (resid 95 through 119 )CB95 - 11978 - 102
1212chain 'C' and (resid 120 through 134 )CB120 - 134103 - 117
1313chain 'B' and (resid 1 through 17 )BC1 - 171 - 17
1414chain 'D' and (resid 1 through 17 )DE1 - 171 - 17
1515chain 'E' and (resid 18 through 119 )EG18 - 1191 - 102
1616chain 'E' and (resid 120 through 134 )EG120 - 134103 - 117
1717chain 'F' and (resid 1 through 17 )FH1 - 171 - 17
1818chain 'G' and (resid 18 through 26 )GJ18 - 261 - 9
1919chain 'G' and (resid 27 through 35 )GJ27 - 3510 - 18
2020chain 'G' and (resid 36 through 52 )GJ36 - 5219 - 35
2121chain 'G' and (resid 53 through 68 )GJ53 - 6836 - 51
2222chain 'G' and (resid 69 through 78 )GJ69 - 7852 - 61
2323chain 'G' and (resid 79 through 84 )GJ79 - 8462 - 67
2424chain 'G' and (resid 85 through 94 )GJ85 - 9468 - 77
2525chain 'G' and (resid 95 through 101 )GJ95 - 10178 - 84
2626chain 'G' and (resid 102 through 109 )GJ102 - 10985 - 92
2727chain 'G' and (resid 110 through 131 )GJ110 - 13193 - 114
2828chain 'H' and (resid 1 through 17 )HK1 - 171 - 17
2929chain 'I' and (resid 18 through 41 )IM18 - 411 - 24
3030chain 'I' and (resid 42 through 52 )IM42 - 5225 - 35
3131chain 'I' and (resid 53 through 68 )IM53 - 6836 - 51
3232chain 'I' and (resid 69 through 84 )IM69 - 8452 - 67
3333chain 'I' and (resid 85 through 101 )IM85 - 10168 - 84
3434chain 'I' and (resid 102 through 133 )IM102 - 13385 - 116
3535chain 'J' and (resid 1 through 17 )JN1 - 171 - 17
3636chain 'K' and (resid 18 through 41 )KP18 - 411 - 24
3737chain 'K' and (resid 42 through 52 )KP42 - 5225 - 32
3838chain 'K' and (resid 53 through 68 )KP53 - 6833 - 48
3939chain 'K' and (resid 69 through 78 )KP69 - 7849 - 58
4040chain 'K' and (resid 79 through 101 )KP79 - 10159 - 81
4141chain 'K' and (resid 102 through 133 )KP102 - 13382 - 113
4242chain 'L' and (resid 1 through 17 )LQ1 - 171 - 17

+
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://pdbjlvh1.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