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Basic information

Entry
Database: PDB / ID: 6qd6
TitleMolecular scaffolds expand the nanobody toolkit for cryo-EM applications: crystal structure of Mb-cHopQ-Nb207
ComponentsMb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207
KeywordsSTRUCTURAL PROTEIN / Scaffold
Function / homologySabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Outer membrane protein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.84 Å
AuthorsUchanski, T. / Masiulis, S. / Fischer, B. / Kalichuk, V. / Wohlkonig, A. / Zogg, T. / Remaut, H. / Vranken, W. / Aricescu, A.R. / Pardon, E. / Steyaert, J.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders Belgium
Grenoble Instruct-ERIC Center Belgium
CitationJournal: Nat.Methods / Year: 2021
Title: Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM
Authors: Uchanski, T. / Masiulis, S. / Fischer, B. / Kalichuk, V. / Lopez-Sanchez, U. / Zarkadas, E. / Weckener, M. / Sente, A. / Ward, P. / Wohlkonig, A. / Zogg, T. / Remaut, H. / Naismith, J.H. / ...Authors: Uchanski, T. / Masiulis, S. / Fischer, B. / Kalichuk, V. / Lopez-Sanchez, U. / Zarkadas, E. / Weckener, M. / Sente, A. / Ward, P. / Wohlkonig, A. / Zogg, T. / Remaut, H. / Naismith, J.H. / Nury, H. / Vranken, W. / Aricescu, A.R. / Pardon, E. / Steyaert, J.
History
DepositionDec 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207
B: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207
C: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207
D: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207
E: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207
F: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207
G: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207
H: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207
I: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207
J: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207
hetero molecules


Theoretical massNumber of molelcules
Total (without water)580,53211
Polymers580,49610
Non-polymers351
Water2,054114
1
A: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0852
Polymers58,0501
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207


Theoretical massNumber of molelcules
Total (without water)58,0501
Polymers58,0501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207


Theoretical massNumber of molelcules
Total (without water)58,0501
Polymers58,0501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207


Theoretical massNumber of molelcules
Total (without water)58,0501
Polymers58,0501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207


Theoretical massNumber of molelcules
Total (without water)58,0501
Polymers58,0501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207


Theoretical massNumber of molelcules
Total (without water)58,0501
Polymers58,0501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207


Theoretical massNumber of molelcules
Total (without water)58,0501
Polymers58,0501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207


Theoretical massNumber of molelcules
Total (without water)58,0501
Polymers58,0501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207


Theoretical massNumber of molelcules
Total (without water)58,0501
Polymers58,0501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207


Theoretical massNumber of molelcules
Total (without water)58,0501
Polymers58,0501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.170, 92.920, 244.220
Angle α, β, γ (deg.)92.05, 96.93, 112.15
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207


Mass: 58049.621 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria), (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Gene: C2R84_04360, hopQ, HPG27_1120 / Strain: G27 / Production host: Escherichia coli (E. coli) / References: UniProt: B5Z8H1
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.58 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.2 M ammonium citrate, 17 % PEG3350, 10 % Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.84→41.45 Å / Num. obs: 129248 / % possible obs: 95.6 % / Redundancy: 1.78 % / Biso Wilson estimate: 97.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.055 / Net I/σ(I): 11.65
Reflection shellResolution: 2.84→2.9 Å / Redundancy: 1.76 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 7733 / CC1/2: 0.854 / Rrim(I) all: 0.663 / % possible all: 94.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.84→41.45 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.511 / SU Rfree Blow DPI: 0.332
RfactorNum. reflection% reflectionSelection details
Rfree0.239 6538 5.06 %RANDOM
Rwork0.204 ---
obs0.206 129248 95.5 %-
Displacement parametersBiso mean: 99.89 Å2
Baniso -1Baniso -2Baniso -3
1--4.4392 Å2-1.3114 Å21.5186 Å2
2--1.9321 Å2-0.4157 Å2
3---2.507 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 2.84→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33038 0 1 105 33144
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0133550HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2645439HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d11592SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes5816HARMONIC5
X-RAY DIFFRACTIONt_it33550HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion23.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4595SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact37870SEMIHARMONIC4
LS refinement shellResolution: 2.84→2.86 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2485 129 4.99 %
Rwork0.2332 2456 -
all0.234 2585 -
obs--86.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.06830.0868-0.01145.24430.16740.20590.2347-0.0216-0.0014-0.339-0.241-0.6709-0.27170.24440.0064-0.02320.00710.0381-0.12880.0922-0.124150.163450.426-86.2236
23.2829-1.8212-0.08757.1417-1.32161.19690.2609-0.2626-0.48770.0195-0.3975-0.3456-0.12430.07310.1366-0.06270.0061-0.1465-0.06520.10050.077746.957428.1354-80.562
39.7964-2.12132.76956.4983-1.17741.23330.06130.1387-0.35740.1235-0.12140.07980.09420.18650.0602-0.1250.16170.0139-0.18280.08130.017453.8782-5.6323-70.8564
41.12331.4179-0.62877.1184-1.44020.48350.1312-0.3227-0.4420.7595-0.3362-0.0149-0.20090.00810.205-0.124-0.1295-0.0954-0.17430.0906-0.052226.57125.6629-60.1005
51.20830.5587-0.75235.4453-2.03541.79380.0823-0.4136-0.2740.2711-0.33180.2542-0.1208-0.11130.2495-0.0718-0.1451-0.0199-0.08740.06560.121226.7821-1.0787-62.1639
60.83141.3070.29995.93711.62880.4830.0587-0.06730.0821-0.0139-0.12870.31480.02940.01080.07-0.06030.0026-0.0593-0.12060.01010.007833.829441.145-64.9015
71.0072-1.63080.77558.1022-2.36660.6480.18550.30780.3004-0.4044-0.37470.34430.15360.0320.1892-0.11030.18520.135-0.16340.0864-0.0432-9.745827.492-36.9595
83.20920.6147-1.79497.96322.82343.59410.2351-0.0647-0.0332-0.4615-0.31520.07570.46390.04540.08010.16520.22060.1647-0.1980.0175-0.1751-4.18365.8479-35.3185
90.536-0.5977-0.23286.42821.02150.34780.00640.119-0.0650.2491-0.15440.5460.0883-0.01780.148-0.07830.01490.1054-0.09250.01370.0585-1.5654-12.4989-31.3504
101.29291.2594-0.20976.7958-0.50920.74130.1111-0.0422-0.0607-0.0904-0.2279-0.65790.39160.29910.1168-0.15350.03380.132-0.03660.1116-0.132813.6824-8.1742-16.2329
111.64190.2564-0.37043.77750.98440.22160.193-0.12060.05810.5069-0.1406-0.52360.27050.2687-0.0524-0.04-0.0404-0.0069-0.16010.1529-0.118313.9282-15.957-10.7621
127.05322.2268-1.27289.7641-1.65721.32360.0672-0.23270.3769-0.09050.025-0.06070.00510.0516-0.0922-0.1828-0.14040.0716-0.17030.09410.064419.036237.0519-26.356
131.0374-0.3598-0.22987.0776-1.34051.39640.22730.29370.3866-0.58710.05010.6745-0.111-0.539-0.2775-0.2417-0.02850.0901-0.03680.0153-0.14995.832571.868615.9932
144.0791.9448-0.32054.7942-2.34692.10590.02060.3426-0.1276-0.49710.05480.47020.3432-0.2949-0.0755-0.0844-0.19790.0861-0.0655-0.1124-0.20789.417953.516521.0226
155.05611.68971.4049.08622.33938.9769-0.0340.00320.0362-0.30020.03940.22610.36060.0931-0.0054-0.0976-0.15670.1477-0.1732-0.0827-0.10137.631617.839523.6112
160.10990.3286-0.26988.2835-2.48610.76070.2416-0.1086-0.224-0.0888-0.6595-0.7815-0.08060.24960.4179-0.1375-0.29390.0106-0.0370.13530.008734.931322.624935.9691
170.72170.3849-0.38078.921-1.30630.24660.2287-0.0641-0.1465-0.0037-0.4583-0.7157-0.13420.13930.2295-0.1557-0.27430.0668-0.02370.04350.045832.553426.136835.7524
180.84321.7715-0.86476.6985-2.9522.53320.1309-0.068-0.01830.2584-0.26450.128-0.32470.09020.1336-0.0281-0.18120.0743-0.0681-0.0559-0.15932.211265.603620.1961
191.2391-1.6955-0.47297.06850.57620.14640.23770.13020.3301-0.3619-0.0642-0.5198-0.0103-0.0897-0.1735-0.21030.05180.02220.1617-0.083-0.19460.1716.741260.8813
200.9942-0.4862-0.49577.62362.51931.78330.16920.25380.3937-0.4339-0.1027-0.1073-0.31780.0372-0.0666-0.14970.14340.1174-0.01180.0393-0.066-4.179637.531663.458
211.1197-1.3414-0.86775.03691.31510.9603-0.0281-0.0143-0.1270.1372-0.0572-0.14130.1456-0.44890.0853-0.2008-0.0448-0.05680.1112-0.0552-0.09051.1386-10.124657.5526
221.2972-0.2994-0.55955.23490.7370.2497-0.1482-0.3592-0.17190.7034-0.2677-0.59940.2577-0.12750.41590.0493-0.0053-0.0717-0.08630.1359-0.24933.2005-20.924982.658
231.7952-1.5413-0.19972.52571.90571.2511-0.1984-0.1707-0.20520.6285-0.2496-0.11950.2545-0.10250.44810.0991-0.04220.064-0.08680.1875-0.26191.1059-25.43680.1321
241.83091.19830.76367.45761.03170.5851-0.178-0.50190.44540.4243-0.24990.0690.013-0.3880.4279-0.02710.0529-0.03040.1027-0.1221-0.33113.387317.745986.1701
25-0.09231.591-0.49315.5031-1.02220.14640.0238-0.087-0.16150.3141-0.185-0.6456-0.23420.1060.1611-0.02050.1359-0.2193-0.25220.05750.2024.381476.357104.3344
261.1980.9390.4277.72740.09550.25460.151-0.1639-0.13010.2146-0.2855-0.3735-0.0261-0.15660.13450.0690.1983-0.1849-0.16470.08590.0616-1.06154.6937109.3282
274.567-1.4833.35454.4024-2.02847.0528-0.01490.0343-0.1505-0.2688-0.02040.16510.12270.11920.03530.1120.2154-0.0355-0.1708-0.0256-0.14424.283620.8095129.8892
282.30790.38750.2995.3964-0.68842.39540.2197-0.452-0.41360.47260.22420.5225-0.0694-0.6714-0.4439-0.22750.108-0.1-0.07730.1174-0.0768-24.373126.6238127.9844
292.7771-0.35970.5264.3386-2.53771.72130.2508-0.1394-0.2780.05190.11230.4728-0.1587-0.6688-0.3631-0.18160.1562-0.1098-0.1367-0.0273-0.1186-22.230930.6813122.0656
302.7567-1.61820.2467.81881.50748.7647-0.050.20110.3006-0.63220.0401-0.00620.14910.06340.00990.27560.1956-0.0691-0.2392-0.058-0.1588-21.633277.961120.8048
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|3 - 322}
2X-RAY DIFFRACTION2{A|323 - 419}
3X-RAY DIFFRACTION3{A|420 - 534}
4X-RAY DIFFRACTION4{B|1 - 211}
5X-RAY DIFFRACTION5{B|212 - 346}
6X-RAY DIFFRACTION6{B|347 - 532}
7X-RAY DIFFRACTION7{C|1 - 321}
8X-RAY DIFFRACTION8{C|322 - 385}
9X-RAY DIFFRACTION9{C|386 - 532}
10X-RAY DIFFRACTION10{D|2 - 121}
11X-RAY DIFFRACTION11{D|122 - 417}
12X-RAY DIFFRACTION12{D|418 - 532}
13X-RAY DIFFRACTION13{E|1 - 307}
14X-RAY DIFFRACTION14{E|308 - 419}
15X-RAY DIFFRACTION15{E|420 - 532}
16X-RAY DIFFRACTION16{F|1 - 232}
17X-RAY DIFFRACTION17{F|250 - 382}
18X-RAY DIFFRACTION18{F|383 - 532}
19X-RAY DIFFRACTION19{G|2 - 109}
20X-RAY DIFFRACTION20{G|110 - 338}
21X-RAY DIFFRACTION21{G|339 - 532}
22X-RAY DIFFRACTION22{H|1 - 208}
23X-RAY DIFFRACTION23{H|209 - 393}
24X-RAY DIFFRACTION24{H|394 - 532}
25X-RAY DIFFRACTION25{I|1 - 330}
26X-RAY DIFFRACTION26{I|331 - 419}
27X-RAY DIFFRACTION27{I|420 - 533}
28X-RAY DIFFRACTION28{J|1 - 204}
29X-RAY DIFFRACTION29{J|205 - 419}
30X-RAY DIFFRACTION30{J|420 - 532}

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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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