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- PDB-7mfu: Crystal structure of synthetic nanobody (Sb14+Sb68) complexes wit... -

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Basic information

Entry
Database: PDB / ID: 7mfu
TitleCrystal structure of synthetic nanobody (Sb14+Sb68) complexes with SARS-CoV-2 receptor binding domain
Components
  • Spike protein S1
  • Synthetic Nanobody #14 (Sb14)
  • Synthetic nanobody #68 (Sb68)
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Spike Protein / Receptor Binding Domain / RBD / Antibody / Nanobody / Sybody / Complex / Neutralization / Epitope
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJiang, J. / Ahmad, J. / Natarajan, K. / Boyd, L.F. / Margulies, D.H.
CitationJournal: J Biol Chem / Year: 2021
Title: Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction.
Authors: Javeed Ahmad / Jiansheng Jiang / Lisa F Boyd / Allison Zeher / Rick Huang / Di Xia / Kannan Natarajan / David H Margulies /
Abstract: Combating the worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the emergence of new variants demands understanding of the structural basis of the interaction of ...Combating the worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the emergence of new variants demands understanding of the structural basis of the interaction of antibodies with the SARS-CoV-2 receptor-binding domain (RBD). Here, we report five X-ray crystal structures of sybodies (synthetic nanobodies) including those of binary and ternary complexes of Sb16-RBD, Sb45-RBD, Sb14-RBD-Sb68, and Sb45-RBD-Sb68, as well as unliganded Sb16. These structures reveal that Sb14, Sb16, and Sb45 bind the RBD at the angiotensin-converting enzyme 2 interface and that the Sb16 interaction is accompanied by a large conformational adjustment of complementarity-determining region 2. In contrast, Sb68 interacts at the periphery of the SARS-CoV-2 RBD-angiotensin-converting enzyme 2 interface. We also determined cryo-EM structures of Sb45 bound to the SARS-CoV-2 spike protein. Superposition of the X-ray structures of sybodies onto the trimeric spike protein cryo-EM map indicates that some sybodies may bind in both "up" and "down" configurations, but others may not. Differences in sybody recognition of several recently identified RBD variants are explained by these structures.
History
DepositionApr 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Advisory / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms / struct
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Oct 20, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike protein S1
B: Synthetic Nanobody #14 (Sb14)
C: Synthetic nanobody #68 (Sb68)
D: Spike protein S1
E: Synthetic Nanobody #14 (Sb14)
F: Synthetic nanobody #68 (Sb68)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,30315
Polymers96,7146
Non-polymers5899
Water17,330962
1
A: Spike protein S1
B: Synthetic Nanobody #14 (Sb14)
C: Synthetic nanobody #68 (Sb68)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6357
Polymers48,3573
Non-polymers2784
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Spike protein S1
E: Synthetic Nanobody #14 (Sb14)
F: Synthetic nanobody #68 (Sb68)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6678
Polymers48,3573
Non-polymers3105
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.820, 83.050, 92.830
Angle α, β, γ (deg.)90.000, 106.711, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Spike protein S1


Mass: 22115.834 Da / Num. of mol.: 2 / Fragment: Receptor Binding Domain (RBD)
Source method: isolated from a genetically manipulated source
Details: RECEPTOR BINDING DOMAIN
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC2

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Antibody , 2 types, 4 molecules BECF

#2: Antibody Synthetic Nanobody #14 (Sb14)


Mass: 12550.034 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21b / Production host: Escherichia coli MC1061 (bacteria)
#3: Antibody Synthetic nanobody #68 (Sb68)


Mass: 13691.096 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21b / Production host: Escherichia coli MC1061 (bacteria)

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Non-polymers , 3 types, 971 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 962 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 8000, 0.1M Hepes pH 7.5 / PH range: 5.5 -7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40.27 Å / Num. obs: 105129 / % possible obs: 98.44 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 20.3 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.057 / Rrim(I) all: 0.104 / Net I/av σ(I): 8.87 / Net I/σ(I): 8.87
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 1.71 / Num. unique obs: 9993 / CC1/2: 0.64 / CC star: 0.88 / Rpim(I) all: 0.51 / Rrim(I) all: 0.925 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KLW

7klw


Resolution: 1.7→40.27 Å / SU ML: 0.1994 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.8564
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2149 5257 5 %
Rwork0.1811 99872 -
obs0.1828 105129 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.88 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6768 0 38 962 7768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00447008
X-RAY DIFFRACTIONf_angle_d0.73449533
X-RAY DIFFRACTIONf_chiral_restr0.05091017
X-RAY DIFFRACTIONf_plane_restr0.00491231
X-RAY DIFFRACTIONf_dihedral_angle_d17.83322442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.34531660.29293137X-RAY DIFFRACTION92.26
1.72-1.740.28021660.26973164X-RAY DIFFRACTION94.44
1.74-1.760.3271680.25133192X-RAY DIFFRACTION94.75
1.76-1.780.25251660.22593163X-RAY DIFFRACTION94.07
1.78-1.810.26631710.22713242X-RAY DIFFRACTION94.88
1.81-1.830.27131740.22543308X-RAY DIFFRACTION99.63
1.83-1.860.26051760.22093343X-RAY DIFFRACTION99.07
1.86-1.890.29691760.22333339X-RAY DIFFRACTION99.46
1.89-1.910.27011760.22233340X-RAY DIFFRACTION99.35
1.91-1.950.23861760.20693354X-RAY DIFFRACTION99.46
1.95-1.980.27031750.20043324X-RAY DIFFRACTION98.67
1.98-2.020.24021750.20323316X-RAY DIFFRACTION97.98
2.02-2.050.23591720.18723270X-RAY DIFFRACTION98.46
2.05-2.10.22881780.1813381X-RAY DIFFRACTION99.41
2.1-2.140.2221770.18413368X-RAY DIFFRACTION99.75
2.14-2.190.22621760.18543331X-RAY DIFFRACTION98.9
2.19-2.250.21311760.17483344X-RAY DIFFRACTION99.58
2.25-2.310.22831790.17983401X-RAY DIFFRACTION99.69
2.31-2.380.22711760.18293359X-RAY DIFFRACTION99.75
2.38-2.450.23271770.18713353X-RAY DIFFRACTION99.77
2.45-2.540.24631770.1943372X-RAY DIFFRACTION99.61
2.54-2.640.26071780.19193371X-RAY DIFFRACTION99.61
2.64-2.760.24121760.18533355X-RAY DIFFRACTION99.55
2.76-2.910.21061760.18573345X-RAY DIFFRACTION98.19
2.91-3.090.2131780.17533367X-RAY DIFFRACTION99.83
3.09-3.330.17561790.1733401X-RAY DIFFRACTION99.67
3.33-3.660.16971780.16063398X-RAY DIFFRACTION100
3.66-4.190.19141790.15243387X-RAY DIFFRACTION99.78
4.19-5.280.16161790.14223406X-RAY DIFFRACTION99.61
5.28-40.270.19391810.18343441X-RAY DIFFRACTION98.5
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)
19.289533570182.90521580025-0.3897298291965.238419077541.293308997536.61260351770.215430335982-1.12840881546-0.756172833812-0.191742716821-0.1352807670761.070339069480.102875745238-0.843542487796-0.0775791501250.230923616426-0.0671187703097-0.02041651236960.3471290110560.07921574018650.419912294128-29.4866209334-11.202559557-29.0921287715
26.19644816584-2.25092220975-2.089636643342.67639702270.5723820169615.42319288309-0.0145348533061-0.240067977082-0.6012743108070.0591899088222-0.01649371510610.4173712880370.0152554082803-0.2141277745660.04479993923570.130991383575-0.02805588373050.02573664450680.09815635347830.02827493221840.277334876078-17.9537636608-17.2588580568-35.4591460158
35.808045350774.592174909760.2112252630556.20642863231.430390067561.237374914280.0159418918286-0.3675056983390.4280695342150.22636369617-0.1379790772380.763298780860.0478684767476-0.2840025604130.09982024783550.1601116261350.005313455581040.03813145059040.1677381340290.00892173381960.221798732382-25.3517849845-2.98638042416-29.6979676795
46.1654230668-0.222475645145-0.7009758498482.98976488925-0.05532305413381.669912593080.02599192480360.130161399270.159129145208-0.10520624196-0.006434701655930.394070373698-0.139206198053-0.183914586202-0.01752201833370.1180193260990.00305931407388-0.007696778300850.127208746593-0.003091228436560.141150036787-19.6678724165-4.05986126036-38.4983163553
52.00561692903-0.6791865214660.7131736376231.88770806351-0.01137395715713.50348288206-0.01222060980850.08254719233440.066040679958-0.157908387436-0.01328238219260.0954282427235-0.176361738393-0.1229535380370.01811309081680.0898843601007-0.015375253133-0.001750800350170.08433925798180.00670671418510.173054464323-11.8992489959-8.28204850162-40.9099633532
62.76538247840.5743921107252.967293100891.182616372260.510254804096.964098144530.1548904679720.0260989431229-0.2999647886080.05581272265420.015889086484-0.1479867750580.4387319887720.23316131823-0.2223926897880.1265209371590.0177504463511-0.006885954548840.0964259001240.008918204750860.219863041563-2.44135201437-19.4730286511-37.8256312174
75.4729301749-1.8945853765-1.069645263332.57222811733-0.5556888078180.943235708726-0.05433878283520.583678421983-0.62246963902-0.200488909257-0.0115185063280.1146741086520.2553422737880.05187485630230.04024576767150.209591869846-0.016211730116-0.02880330647910.215948125409-0.1121225663270.238033274048-6.59337867665-22.8410071843-51.1664411624
81.98177478747-0.05208264663540.15088478621.756230844070.3708840021421.14530407433-0.01558822096720.0562946543223-0.235104139402-0.1013646461870.1141868491950.003265107058320.07566924243480.0382783011927-0.09780915508690.0971588248596-0.01976654400440.01658590192590.1164248338280.0140227086860.154354036218-3.33879941538-16.8788362609-38.8139845357
98.919729696730.4527161295250.05372633908037.248050191233.449192751342.027749418570.06894527783310.845557873537-0.412626816168-0.704799852181-0.6706145953441.05187534498-0.519002313688-0.7112330419970.6287223616970.2776471287010.0813137494068-0.1130476673070.30722117432-0.08145468168410.491981734475-36.9234745678-5.75300654776-40.9449605651
109.59083577663-2.793389365644.696112661747.53521066435-2.774454692269.28017432730.4702358874850.9621801410340.109636745713-0.628782902956-0.665682456616-0.4347851022610.289377744750.4837163916150.1714088072650.1840083312790.07127318628160.04420126476740.228966947022-0.001588314485640.17591210894914.237089353-13.1949103103-52.2721335591
113.94372488832.1433428147-1.465647953183.399245977633.258354087327.872002872430.151480297469-0.501202965616-0.05614303315390.4030605936670.226456629537-0.6274625624990.4629717430380.883278349836-0.2325089619470.1622762970250.0635692035041-0.04870820302960.2838405880310.01613419946440.26947820557326.268137215-20.7439196776-34.5114589232
129.80471128276-7.18579842138.717586060018.24954696873-8.504317554579.478587733430.3157584936250.4740253474770.259764793288-0.237978103084-0.39874706331-0.179990987530.1340537204130.5314956112030.09893125499030.1574918724220.004754507067230.03830242856450.1540812257110.001624527636960.20894811740918.8812192154-11.1228024906-44.9536348807
135.90344200078-3.258102187040.02553286122374.99853749517-4.137352650372.044123162220.2450166991750.2367577177380.8777410073750.2076823664040.0732617502663-0.0182314596218-0.449830810524-0.40515771744-0.3051456903130.1948333922970.0122657354216-0.0002661604049240.1562906356370.01744288992870.2378371565927.8576566062-3.3271522938-48.8587383911
145.44077624012-1.219431982381.095142322974.49169875781-0.4109610566375.795939841220.1130635144180.0400021078673-0.5482933572770.226396495006-0.0912914117564-0.04721934750620.223797897621-0.0622167188853-0.0258404808880.1119073492190.02823955234790.00302913828790.1327412336530.02520003657390.1803318694169.09770575165-20.9572549298-39.9556475437
154.37863253864-1.063589464910.4082142004483.99383718215-0.5697188070494.229791821640.0883269038097-0.02821161257260.2399801935110.202406691872-0.0966995761280.151301550776-0.298670199218-0.0787193870844-0.002496782116690.102420820939-0.003733092592130.03715776476140.115744797751-0.005988897440260.1336096549778.63927675047-9.68645979048-33.5580435314
163.896828172890.276441349002-0.4448260418675.49323165866-3.808676392789.456107557710.08436712334730.1745015215810.6310140260330.126097311147-0.22313439188-0.314512879844-0.5696327075110.4376722881020.1211177515390.12728143462-0.02186469392140.02927413837630.1684775830310.01404864538450.22154060224517.4231418384-6.34646054515-41.2976706249
177.195490967376.755181735796.195865057372.025595608567.366442462542.064350052380.23835867885-0.500333849111-0.1182114526630.38986980026-0.331310291642-0.02263124355940.114174833641-0.2518448880460.1338132554480.264587551715-0.01657771867170.007216363081340.2257668286350.03310235616350.19562038697519.611465331-20.8253643473-30.6137709018
187.54241038236-3.558877422932.594486968374.30574142724-1.542542742522.358839621180.07141269263430.18829552485-0.0724599906420.0186970260456-0.0551989664864-0.1189475163390.04231745928680.0574277815177-0.03113955616650.09252866423220.003209173586990.02804461733340.1231084699190.002173196142570.13304605444112.0212272353-18.0911839931-45.0709357626
199.132775721894.993398844966.230900134089.127266110534.13968367658.879301207960.04606411460110.6066876152580.83035300193-0.389598117632-0.1553537317980.0890317271953-0.3043607297520.2763639051950.07847089134020.223100526210.0409747432190.07007315388270.1791930193630.03507684187140.338322951469-12.852890343921.3319836391-41.4162536815
207.856051326261.881771176216.585224034233.10281149005-0.3104231598686.95080074635-0.0143265085446-0.3318689978410.48476870450.363634588628-0.2740370238960.18120563537-0.2404053868980.03521522023840.2654994902540.321960708851-0.0961119797630.008360303505650.296969048469-0.08343621852330.2693285889475.6547476434124.7758975063-25.5882112243
217.644948547692.262126514515.679819423122.778085537061.176880629442.10234311395-0.226634964241-0.5384319920480.7557466020950.0928808536347-0.0332581146490.024214188291-0.37177046646-0.2021173640580.07585193842020.1550309668390.01013589638580.01163594858060.292703562254-0.06444496687040.301757214422-9.322101135323.0994694406-31.8454473901
223.769288457841.64476930264-0.7021585722932.64937565899-1.136390860532.269524074390.0784290281965-0.110245781134-0.0653985242779-0.0845599385473-0.01237592505950.0146641034181-0.05643774134670.112110831469-0.06766879588480.133310650783-0.01729461633430.01690156299440.0809967011002-0.003549416029020.148864628205-6.4853859282312.368699311-35.2602029566
232.02981318416-0.3704866689051.483635058583.57690085714-0.9045528777082.90424677725-0.07776253954-0.542029099206-0.3224294302170.313827879895-0.01869830496160.125754162759-0.02572638465290.02502246632720.05095977756440.178000358246-0.006441050517260.03076483452970.1864539125440.002968967702350.183372334096-9.625032627198.40307456122-25.4880835824
248.64953221255-3.775531680625.497718095035.76191188178-2.759122900749.03196771703-0.206668286213-0.814140615914-0.004728269731010.2982912169190.1512268850630.117518538361-0.352256135226-0.2999658985680.03515598761670.214724698178-0.0355681087130.04331094996190.180681938755-0.02765995646340.129843436898-6.2841393897415.4363821496-23.4919492326
256.9837425963-4.521200494445.432737246028.50124775559-2.601264497589.030080254-0.391137901651-0.7119087287180.0732609557190.4386800711670.301309337810.848580440036-0.6151581958-0.7819676033070.06135673727420.2499085467390.04085175541410.07010101396850.256062794956-0.07862668823830.271765170832-11.755965091121.7058024998-27.6256107063
269.46790229874.26552583048-4.899539173875.84211068771.634333192582.02240659937-0.0421542940566-1.22056307674-0.4885544082840.620064240979-0.0673906082539-0.6983603167620.3309868649760.867824297680.08089784975810.1880630674620.00928953004268-0.06190089945940.3478216624740.05246092511370.2156195999157.1164711006516.9573087116-25.4487607873
274.671600374313.955253621551.402732758884.599666251270.5743522110491.62174835188-0.1875755567460.2185410703660.00762982097695-0.2243513648880.184680996181-0.0904655609324-0.04058794967640.115385707418-0.002694512585780.09605405962870.007870318251510.03250498889110.134148041366-0.0003465107416280.139272433089-7.628861452310.0701755874-36.3174047362
285.940517397573.015120965590.3659981503382.046151352860.9556574267532.78408545048-0.01098750945210.1935920036760.405152333044-0.361373516077-0.08227005045720.196784836304-0.02638677819820.2379957985780.06483873037910.181967551844-0.005575877379670.01730233695020.1599860838020.06595300131440.174468541688-9.0383486031913.0535717268-42.3642085497
292.017046628762.05464653418.971553438296.325371528270.297053398582.05625075464-0.116181936591-0.337213362920.371512365329-0.0962016279378-0.0155574115885-0.275587518738-0.4347398225630.5101428847230.1539035326630.175547270708-0.1048200751080.04563749178670.359519940145-0.05514419124350.2344314211517.2777566764922.4883884723-31.232293843
302.012064227960.426376132287-1.798224461086.244276487161.061280614995.30810974013-0.2747094990460.4008889266761.096065502560.04188498489240.1423141646750.948816900421-0.210205392292-0.9330175671770.1293227352590.2046175676720.06574177995840.008981893495190.322719783850.05488329866440.328846745744-9.20929855301-13.5455742664-14.9474951245
310.5098170490620.8021876472730.7396584026831.71276923550.6092762953262.9368067155-0.02338411754280.1411145278050.4451106257240.005856535558890.004791610345410.268419868683-0.0633939037299-0.2530943861970.02836861468130.1042912719430.02869106006230.00541362008970.1589044952470.01586432331510.2717009171242.16858311118-7.58904675288-8.77531728798
327.61231631839-6.1095864872-1.316737053936.755886369291.97741502661.345719695430.04699340091980.389053805026-0.31105727034-0.0615693004408-0.1806673006750.6980772358090.0176963701874-0.3071265010110.1436677070830.148871988316-0.00991040387253-0.01850741146010.1873246419030.0302517541220.236501316992-5.32886020769-21.8324775214-14.5976055393
331.48710691960.3410116814970.3982629134041.925800603920.4916628138781.805005800250.0728652193748-0.0819921632136-0.0006046139768950.117372959506-0.02942286345820.2309041862340.0740613328527-0.109616100745-0.04520783267970.09018668227750.01206548392990.01128494724670.1141189549940.009430970094480.1635742650954.18838324566-18.8265057865-4.64586969036
342.337060353840.4751697524541.650287917463.610997080761.9415215381.78199983806-0.07708401671130.3227662384570.361332260999-0.3053228633080.131121614174-0.235293397816-0.442710897310.688182827333-0.08684344165950.116990272094-0.03242416134370.01024895901490.2308957918510.006597577233150.3295802978317.8098012764-5.65064304629-6.3952455192
354.250170394463.0681287171.158359811174.653313431270.02662355266621.85785861666-0.0938388136453-0.7104130844830.7412413666830.2747756507890.0133514327072-0.105257425013-0.26851917620.08084660875630.02211020925750.1799211877670.03427564319050.01267663135510.260427235193-0.1474071321780.33978623590213.4499236103-2.133118321446.94316562965
362.85157321037-0.0624325618577-0.2939718545472.862179231480.9024008314091.77355022512-0.0384932807498-0.1267399375980.4057863677740.04393489575950.268887936304-0.269253645899-0.1801959891320.216414699887-0.2231308748260.108545878779-0.00779150176846-0.0006916755095740.183433299101-0.01722692950480.27962577714322.4955382968-4.87602040866-4.38448705846
375.875576232232.48565509103-3.21963620663.38545195849-1.111819982684.110784563580.114816708923-0.04927905959740.7977208147780.1104880123940.1911633008760.414756396694-0.0967765074652-0.115929585914-0.3204679380510.1074508297420.0174601119881-0.01338167487530.1324218243770.02656718813210.1930463334272.43176074996-16.2712460449-8.02957043014
387.65466891637-0.133203332608-0.7368082181583.67216036434-0.04920466555214.602722505070.105594014018-0.8784268421850.3815622452480.384061258343-0.4559392919050.6324374970470.333598422314-0.635517889950.2192732435870.23247300065-0.07163154720810.06508047677620.313093035281-0.04922328232410.415374525994-16.8044275087-19.2614054392-3.88619281149
392.040179317835.33093503112-7.198357672756.76025590586-4.298915546679.610144478370.353311537852-1.00157294746-0.08439554232370.380099717012-0.575260074615-0.17875387097-0.04440059628020.9082873214890.2421722425310.179609354788-0.0206342899522-0.03008724200180.350495551124-0.01762233979070.24718243587233.7782383731-12.27578917438.61975772689
405.213435339292.21016201107-2.424560582382.45937482187-2.585786063825.128032313230.05047921627450.0152458225778-0.2690785633810.0138151364577-0.121607190562-0.354727797325-0.00223423293310.2615661247280.04737554935650.1123492770940.02118594590790.007763814937150.108012228217-0.03851181642670.23941042672637.4382806378-13.5909020984-1.10366627483
417.39037644405-0.8927340025690.1617748641836.051810783633.255712745845.48715721548-0.01084803679560.1742859208810.550515875082-0.178551305927-0.01816142259670.383914963752-0.330389646584-0.07161095069180.01777208633020.0864088147932-0.01495910020220.004350534356030.1546855174510.008781171376090.18341966642829.236500166-4.0275607283-4.30283211169
428.471933666523.54857416022-1.386393011629.06789924834-2.38321372517.363638945230.07715682110070.278779794417-0.0841390260145-0.2400119593560.04749000610410.2629393871960.332655943282-0.123524936249-0.1457868478420.0922088108944-0.0108477497655-0.01115829690510.14591041337-0.0349289733810.1601399904228.8649165485-15.2707439956-10.7071792766
433.98256854559-0.0165684133526-0.590090025126.76050831153-4.113110492152.260298932280.09998820822620.0210871234462-0.621894118139-0.0526833152287-0.182708291228-0.4226799049580.282278508060.453552274780.06852092568830.1647747588640.00553297162781-0.007943097222860.195768742199-0.01100333712450.27199554711737.5497284957-18.6162837195-2.9384048593
447.800788217631.78042259376-3.739339581641.47796462818-0.4044011678483.559530172740.09046295779880.1508812075630.352767050899-0.1567010585630.02157251983830.157560995907-0.1227594536690.00343277696737-0.119377616710.1307916299670.0105646147912-0.01787259798260.1435365583740.01894867929250.20470114428934.1695590267-6.6737127319-5.51037490926
456.777137675923.25195448748-2.606571525434.60693419595-0.8042575518443.648907452750.257748637997-0.09548284199410.8183863955160.1248440047540.02112419458560.0689645653479-0.3164973004460.248492184913-0.3049874553310.100515901450.0190502592341-0.0389958862890.127710936397-0.004365497113170.24805071536833.6765472159-5.6510563010.997696384805
462.05025409147-2.11084598709-6.563285265945.873953427252.99213356429.64556219382-0.0954793005242-0.703738861187-1.012417256170.624986113913-0.2602693500460.1160522529910.6861191373390.3004584979040.3649774372430.270576804973-0.0255404783676-0.0436069477230.2384301030040.06421208345620.4107539555847.22032349215-46.3669243824-3.31257716885
475.77092595633-1.21180337134-0.8321181999582.6190097734-0.3172106618971.606365013380.02366498555640.337312636885-0.589166029006-0.135869097752-0.05820706395250.1124181967160.174924534673-0.01540647789490.02425433727970.1378479658560.0139720047686-0.01619633323030.144159433684-0.01346755611730.1766805429713.452206249-43.9907268791-12.5940183176
482.06495763332-6.068582363177.910758003284.7805909247-3.790977797127.40644256588-0.2048118694710.2031313758860.4995298359010.296225650498-0.0257907396819-0.615698880103-0.2422928733150.4213537223490.3024062085120.1487464048770.00397897755421-0.01102648185150.230657515074-0.003283826309190.28062065934719.3279348843-35.5996680754-9.46635929003
497.198596299060.990191532512-3.021161246665.23417927635-0.002300992784863.22819189769-0.1392948410150.3020751202970.301898394984-0.3561183406130.012592764292-0.0733598780862-0.06665023949660.07774077620660.1255816575640.154211128070.000175822716034-0.01853039729570.1399159638080.04339796706320.13605114067210.5078678985-33.2138174351-19.0672751545
502.141334648134.67032920587-5.238091049377.22473292773-3.004568357989.09881961646-0.1679021251360.636464796826-0.00901941090365-0.3268992091470.1504065603830.4069935316950.470763279326-0.5557257392690.03747650039490.1646350081120.0125109658111-0.04698219716680.217192893702-0.0352354430360.23737524401610.8644107808-43.6136008976-18.8828149043
515.10247285638-3.019254041230.1799924449323.818741336950.04711716036760.6183414912690.05882512195280.243308974650.00357496309073-0.0811497318027-0.0762768256747-0.1684387761180.02631703240370.1815548036880.01750975319870.105512499273-0.00158020037837-0.002640991274550.1657218032630.01378595858090.14090775972116.7578558124-37.0717916276-11.4191956198
526.42694614143-3.0754815282.13193976348.442963115850.9289426916646.856967304260.034783233488-0.44104047627-0.5830135284290.157276971245-0.1590988021520.06037007726360.105155362871-0.04935188807360.1216071372510.126575320972-0.002928379205210.02236687218210.1810977815760.08964351223810.18981870868811.0083337141-37.9648889563-2.2230523636
538.129380372850.402865310565-5.823787123474.78446164683-1.541161740078.08503824278-0.5592099946420.570935541012-0.7785831345140.05705634995640.119530902183-0.4792514903940.6715239892840.5566023846220.485542097330.1558004300330.08504524593310.005006435531520.347665184378-0.0868594700760.33222041328327.3468084174-47.4469045396-13.4604200536
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 332 through 342 )AA332 - 3421 - 11
22chain 'A' and (resid 343 through 358 )AA343 - 35812 - 27
33chain 'A' and (resid 359 through 375 )AA359 - 37528 - 44
44chain 'A' and (resid 376 through 409 )AA376 - 40945 - 78
55chain 'A' and (resid 410 through 442 )AA410 - 44279 - 111
66chain 'A' and (resid 443 through 459 )AA443 - 459112 - 128
77chain 'A' and (resid 460 through 479 )AA460 - 479129 - 148
88chain 'A' and (resid 480 through 516 )AA480 - 516149 - 185
99chain 'A' and (resid 517 through 528 )AA517 - 528186 - 197
1010chain 'B' and (resid 1 through 7 )BB1 - 71 - 7
1111chain 'B' and (resid 8 through 17 )BB8 - 178 - 17
1212chain 'B' and (resid 18 through 25 )BB18 - 2518 - 27
1313chain 'B' and (resid 26 through 33 )BB26 - 3328 - 35
1414chain 'B' and (resid 34 through 45 )BB34 - 4536 - 47
1515chain 'B' and (resid 46 through 67 )BB46 - 6748 - 69
1616chain 'B' and (resid 68 through 83 )BB68 - 8370 - 85
1717chain 'B' and (resid 84 through 91 )BB84 - 9186 - 93
1818chain 'B' and (resid 92 through 115 )BB92 - 11594 - 119
1919chain 'C' and (resid -1 through 7 )CC-1 - 71 - 9
2020chain 'C' and (resid 8 through 17 )CC8 - 1710 - 19
2121chain 'C' and (resid 18 through 26 )CC18 - 2620 - 30
2222chain 'C' and (resid 27 through 52 )CC27 - 5231 - 56
2323chain 'C' and (resid 53 through 64 )CC53 - 6457 - 68
2424chain 'C' and (resid 65 through 73 )CC65 - 7369 - 77
2525chain 'C' and (resid 74 through 83 )CC74 - 8378 - 87
2626chain 'C' and (resid 84 through 91 )CC84 - 9188 - 95
2727chain 'C' and (resid 92 through 109 )CC92 - 10996 - 115
2828chain 'C' and (resid 110 through 118 )CC110 - 118116 - 124
2929chain 'C' and (resid 119 through 125 )CC119 - 125125 - 131
3030chain 'D' and (resid 332 through 342 )DD332 - 3421 - 11
3131chain 'D' and (resid 343 through 358 )DD343 - 35812 - 27
3232chain 'D' and (resid 359 through 375 )DD359 - 37528 - 44
3333chain 'D' and (resid 376 through 442 )DD376 - 44245 - 111
3434chain 'D' and (resid 443 through 459 )DD443 - 459112 - 128
3535chain 'D' and (resid 460 through 479 )DD460 - 479129 - 148
3636chain 'D' and (resid 480 through 506 )DD480 - 506149 - 175
3737chain 'D' and (resid 507 through 516 )DD507 - 516176 - 185
3838chain 'D' and (resid 517 through 528 )DD517 - 528186 - 197
3939chain 'E' and (resid 1 through 7 )EE1 - 71 - 7
4040chain 'E' and (resid 8 through 33 )EE8 - 338 - 35
4141chain 'E' and (resid 34 through 45 )EE34 - 4536 - 47
4242chain 'E' and (resid 46 through 67 )EE46 - 6748 - 69
4343chain 'E' and (resid 68 through 83 )EE68 - 8370 - 85
4444chain 'E' and (resid 84 through 99 )EE84 - 9986 - 103
4545chain 'E' and (resid 100 through 115 )EE100 - 115104 - 119
4646chain 'F' and (resid -1 through 7 )FF-1 - 71 - 9
4747chain 'F' and (resid 8 through 39 )FF8 - 3910 - 42
4848chain 'F' and (resid 40 through 52 )FF40 - 5243 - 55
4949chain 'F' and (resid 53 through 64 )FF53 - 6456 - 67
5050chain 'F' and (resid 65 through 83 )FF65 - 8368 - 86
5151chain 'F' and (resid 84 through 109 )FF84 - 10987 - 113
5252chain 'F' and (resid 110 through 118 )FF110 - 118114 - 122
5353chain 'F' and (resid 119 through 125 )FF119 - 125123 - 129

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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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