[English] 日本語
Yorodumi
- PDB-7ndf: Crystal structure of nanobody Nb_MsbA#1 in complex with the nucle... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ndf
TitleCrystal structure of nanobody Nb_MsbA#1 in complex with the nucleotide binding domain of MsbA
Components
  • Lipid A ABC transporter ATP-binding protein/permease MsbA
  • Nb_MsbA 1
KeywordsPROTEIN BINDING / nucleotide binding domain / ABC transporter / nanobody
Function / homology:
Function and homology information
Biological speciesVicugna pacos (alpaca)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMeier, G. / Seeger, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_188817 Switzerland
CitationJournal: Sci Adv / Year: 2022
Title: The ABC transporter MsbA adopts the wide inward-open conformation in cells.
Authors: Laura Galazzo / Gianmarco Meier / Dovile Januliene / Kristian Parey / Dario De Vecchis / Bianca Striednig / Hubert Hilbi / Lars V Schäfer / Ilya Kuprov / Arne Moeller / Enrica Bordignon / Markus A Seeger /
Abstract: Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their ...Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their physiological environment. However, to truly understand the biophysical properties of membrane proteins in a physiological environment, they must be investigated within living cells. Here, we used a spin-labeled nanobody to interrogate the conformational cycle of the ABC transporter MsbA by double electron-electron resonance. Unexpectedly, the wide inward-open conformation of MsbA, commonly considered a nonphysiological state, was found to be prominently populated in cells. Molecular dynamics simulations revealed that extensive lateral portal opening is essential to provide access of its large natural substrate core lipid A to the binding cavity. Our work paves the way to investigate the conformational landscape of membrane proteins in cells.
History
DepositionFeb 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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
C: Nb_MsbA 1
D: Nb_MsbA 1
A: Lipid A ABC transporter ATP-binding protein/permease MsbA
B: Lipid A ABC transporter ATP-binding protein/permease MsbA


Theoretical massNumber of molelcules
Total (without water)78,9274
Polymers78,9274
Non-polymers00
Water4,774265
1
C: Nb_MsbA 1
B: Lipid A ABC transporter ATP-binding protein/permease MsbA


Theoretical massNumber of molelcules
Total (without water)39,4632
Polymers39,4632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-5 kcal/mol
Surface area16760 Å2
MethodPISA
2
D: Nb_MsbA 1
A: Lipid A ABC transporter ATP-binding protein/permease MsbA


Theoretical massNumber of molelcules
Total (without water)39,4632
Polymers39,4632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-4 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.530, 99.300, 142.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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

-
Components

#1: Antibody Nb_MsbA 1


Mass: 12337.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein Lipid A ABC transporter ATP-binding protein/permease MsbA


Mass: 27125.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: msbA, HIR41_000141 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A786F4A3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: KSCN, sodium acetate, PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.41 Å / Num. obs: 53394 / % possible obs: 100 % / Redundancy: 13.357 % / Biso Wilson estimate: 43.721 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.101 / Χ2: 0.829 / Net I/σ(I): 23.18 / Num. measured all: 713196 / Scaling rejects: 61
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.1512.3881.3322.2948287389938980.7621.389100
2.15-2.2112.9791.0842.8349165378937880.8111.128100
2.21-2.2813.3380.9373.449379370237020.8880.974100
2.28-2.3514.160.7324.4850834359035900.9410.76100
2.35-2.4214.110.5975.4649229348934890.9480.619100
2.42-2.5113.9990.496.5247150336933680.960.508100
2.51-2.613.9340.3997.8545605327432730.9760.414100
2.6-2.7113.7320.3229.5542693310931090.9810.335100
2.71-2.8313.5220.24512.1641147304430430.9880.255100
2.83-2.9712.9570.18814.8537250287528750.9920.196100
2.97-3.1312.2510.13619.6833912276827680.9950.142100
3.13-3.3212.8470.09128.4633645261926190.9980.094100
3.32-3.5514.0650.06937.7834812247524750.9990.072100
3.55-3.8313.9650.05149.3331979229022900.9990.053100
3.83-4.213.6090.03960.32290282133213310.04100
4.2-4.713.4280.02975.35258751927192710.03100
4.7-5.4212.6230.02972.5217751725172510.03100
5.42-6.6411.4030.03559.26167511469146910.037100
6.64-9.3913.80.02292.73161051167116710.023100
9.39-47.4112.50.015121.96857569368610.01699

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B5W

3b5w


Resolution: 2.1→47.41 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 2669 5 %
Rwork0.2052 50714 -
obs0.2071 53383 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.59 Å2 / Biso mean: 51.0739 Å2 / Biso min: 18.82 Å2
Refinement stepCycle: final / Resolution: 2.1→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5447 0 0 265 5712
Biso mean---47.41 -
Num. residues----707
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.140.32531370.282426132750
2.14-2.180.35141400.276526492789
2.18-2.220.28351380.26726342772
2.22-2.270.33351400.270526512791
2.27-2.320.2761360.234525882724
2.33-2.380.25331390.227926452784
2.38-2.450.2671400.224326692809
2.45-2.520.28261380.235226222760
2.52-2.60.28921400.22426562796
2.6-2.690.29241390.241526372776
2.69-2.80.27441400.229826662806
2.8-2.930.28321400.230626462786
2.93-3.080.23291400.21626642804
3.08-3.280.23981410.214126782819
3.28-3.530.24921410.206326872828
3.53-3.880.25191410.193926742815
3.88-4.450.20071430.173127182861
4.45-5.60.22361450.17227522897
5.6-47.410.19261510.179928653016
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)
15.1288-1.47561.23153.0047-1.76684.0157-0.0862-0.0290.3950.19780.12830.3194-0.1103-0.2383-0.04310.2671-0.02520.04320.2644-0.09290.3886-36.2962.679627.3275
22.4586-1.84031.08984.8935-1.826.58590.0647-0.10230.96010.2841-0.282-0.0995-0.79630.24690.18310.3481-0.06040.01910.2427-0.08970.5756-29.7149.148828.7061
31.84960.0458-0.31480.80750.4734.5042-0.09750.14930.56380.06880.01010.5709-0.5979-0.17270.08280.31040.0033-0.01460.2697-0.02860.5948-38.8565.388123.1706
43.1416-4.073-1.26936.53254.69167.91110.0588-0.1921-0.80350.6576-0.4220.19011.1079-0.54560.40130.87290.0270.05390.38970.02270.663915.6708-60.436423.4192
50.1418-0.58250.08642.3984-0.35560.05150.70160.66460.0587-0.6938-0.3474-0.14190.43210.5118-0.35621.25470.5733-0.20040.859-0.23931.090936.6382-71.720620.3213
65.0604-4.24770.80556.0463-1.63112.39410.18120.472-0.681-0.64260.11940.76620.66090.2523-0.22191.13470.0707-0.07940.2753-0.10360.707222.7695-64.32617.5911
72.8385-1.74251.59257.7222-1.80762.51110.68190.1827-0.9863-0.016-0.06171.37191.42890.4112-0.46360.67780.0267-0.08360.3935-0.00740.558115.2001-52.514213.9409
81.8462-0.2830.90151.5091-1.09121.06180.40040.2376-0.5001-0.0669-0.0739-0.38790.74830.7234-0.16640.57040.3906-0.10380.48520.08880.306331.3955-56.162126.3037
95.30141.1055.90725.65730.73556.63530.33611.0231-0.4752-0.58510.12780.31530.65981.0746-0.58810.52450.25550.04990.63640.02890.423326.8742-51.475813.4325
108.1178-4.16675.91697.4255-2.49666.31950.83350.774-0.9553-0.40010.0366-0.36710.81782.2541-0.99090.63370.33830.01630.9995-0.06430.57435.8268-53.412814.3839
11-0.00040.0229-0.00615.3005-1.66880.52610.06240.3961-0.8012-0.55560.0575-0.37870.55930.9015-0.09870.8170.5394-0.00651.032-0.11320.463531.1342-59.192211.9224
122.7813-3.31090.18376.3733-3.46054.34840.35190.6545-1.23590.14370.14590.52111.82260.6621-0.48240.91410.2048-0.05220.5213-0.11190.51222.7768-62.713112.8428
132.1132-1.2382-0.1432.311-0.32070.11320.15870.27730.2046-0.4728-0.3764-0.36860.33440.4161-0.07821.08210.7058-0.23761.229-0.20280.826340.6139-64.352820.0938
148.1637-1.81322.70672.9376-1.79061.45940.30360.169-1.11460.25560.02760.60471.41640.4397-0.36730.71520.154-0.01610.39090.0870.417823.3645-55.655825.2107
150.91180.14050.22631.4068-0.76670.84620.3060.1137-0.5069-0.26760.0150.36020.26850.13130.08991.10840.5696-0.07840.73890.1020.748534.7359-68.216425.7869
162.7749-1.4376-0.28044.2697-0.13491.4283-0.057-0.1792-0.38280.05120.06930.26070.26320.0423-0.00020.2797-0.0199-0.00860.34680.08250.29354.3978-34.040822.7264
173.76140.1019-0.00926.9753-1.20452.98380.0876-0.43520.31740.2738-0.0308-0.2837-0.07970.0813-0.07420.2809-0.05-0.03380.4383-0.05790.328813.0069-13.087626.1462
184.194-1.6796-0.08082.01131.89915.20270.02610.21070.2429-0.2152-0.0209-0.2525-0.22080.6422-0.00280.3750.00530.0390.38940.17440.374623.223-37.229920.395
193.2322-1.0789-1.12091.20090.54211.8071-0.03340.0617-0.10050.0989-0.05580.0470.1685-0.03960.11260.2686-0.0214-0.03940.36090.01650.2857-9.3424-20.777716.1665
202.74311.9291-1.65676.41813.13276.21640.04860.51860.3102-0.26930.1807-0.3148-0.38590.2403-0.11080.28530.0317-0.01090.42210.03180.24296.8294-18.76223.1722
212.4579-2.0271-1.20832.40131.00451.940.34750.54770.6625-0.4607-0.1942-0.4215-0.27110.2482-0.22440.3273-0.01910.06490.54370.10390.5035-13.3503-4.562311.1991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 45 )C1 - 45
2X-RAY DIFFRACTION2chain 'C' and (resid 46 through 82 )C46 - 82
3X-RAY DIFFRACTION3chain 'C' and (resid 83 through 113 )C83 - 113
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 7 )D1 - 7
5X-RAY DIFFRACTION5chain 'D' and (resid 8 through 17 )D8 - 17
6X-RAY DIFFRACTION6chain 'D' and (resid 18 through 25 )D18 - 25
7X-RAY DIFFRACTION7chain 'D' and (resid 26 through 33 )D26 - 33
8X-RAY DIFFRACTION8chain 'D' and (resid 34 through 45 )D34 - 45
9X-RAY DIFFRACTION9chain 'D' and (resid 46 through 56 )D46 - 56
10X-RAY DIFFRACTION10chain 'D' and (resid 57 through 63 )D57 - 63
11X-RAY DIFFRACTION11chain 'D' and (resid 64 through 72 )D64 - 72
12X-RAY DIFFRACTION12chain 'D' and (resid 73 through 82 )D73 - 82
13X-RAY DIFFRACTION13chain 'D' and (resid 83 through 90 )D83 - 90
14X-RAY DIFFRACTION14chain 'D' and (resid 91 through 107 )D91 - 107
15X-RAY DIFFRACTION15chain 'D' and (resid 108 through 113 )D108 - 113
16X-RAY DIFFRACTION16chain 'A' and (resid 340 through 432 )A340 - 432
17X-RAY DIFFRACTION17chain 'A' and (resid 433 through 527 )A433 - 527
18X-RAY DIFFRACTION18chain 'A' and (resid 528 through 580 )A528 - 580
19X-RAY DIFFRACTION19chain 'B' and (resid 340 through 456 )B340 - 456
20X-RAY DIFFRACTION20chain 'B' and (resid 457 through 497 )B457 - 497
21X-RAY DIFFRACTION21chain 'B' and (resid 498 through 579 )B498 - 579

+
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