[English] 日本語
Yorodumi
- PDB-7a50: Crystal structure of the APH coiled-coil in complex with nanobody Nb26 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7a50
TitleCrystal structure of the APH coiled-coil in complex with nanobody Nb26
Components
  • Coiled-coil APH
  • Nanobody Nb26
KeywordsDE NOVO PROTEIN / coiled-coil / nanobody / antibody / protein design
Biological speciesLama glama (llama)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.999 Å
AuthorsHadzi, S.
Funding supportEuropean Union, Slovenia, 3items
OrganizationGrant numberCountry
European Research Council (ERC)787115European Union
Slovenian Research AgencyP4-0176 Slovenia
Slovenian Research AgencyP1-0201 Slovenia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: A nanobody toolbox targeting dimeric coiled-coil modules for functionalization of designed protein origami structures.
Authors: Majerle, A. / Hadzi, S. / Aupic, J. / Satler, T. / Lapenta, F. / Strmsek, Z. / Lah, J. / Loris, R. / Jerala, R.
History
DepositionAug 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nanobody Nb26
B: Coiled-coil APH
C: Nanobody Nb26
D: Coiled-coil APH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5457
Polymers40,3594
Non-polymers1863
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-28 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.220, 198.220, 58.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 93 or resid 95 through 124))
21(chain C and ((resid 1 and (name CA or name...
12chain B
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNCYSCYS(chain A and (resid 1 through 93 or resid 95 through 124))AA1 - 931 - 93
121ALAALAGLYGLY(chain A and (resid 1 through 93 or resid 95 through 124))AA95 - 12495 - 124
211GLNGLNGLNGLN(chain C and ((resid 1 and (name CA or name...CC11
221GLNGLNGLYGLY(chain C and ((resid 1 and (name CA or name...CC1 - 1241 - 124
231GLNGLNGLYGLY(chain C and ((resid 1 and (name CA or name...CC1 - 1241 - 124
112ACEACENH2NH2chain BBB0 - 411 - 42
212ACEACENH2NH2chain DDD0 - 411 - 42

NCS ensembles :
ID
1
2

-
Components

#1: Antibody Nanobody Nb26


Mass: 15343.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Protein/peptide Coiled-coil APH


Mass: 4835.549 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M calcium chloride, 0.1 M sodium acetate pH 5, 20 % w/v PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.999→43.32 Å / Num. obs: 29399 / % possible obs: 99.52 % / Redundancy: 2.07 % / Biso Wilson estimate: 51.06 Å2 / CC1/2: 0.991 / Rrim(I) all: 0.222 / Net I/σ(I): 8.07
Reflection shellResolution: 1.999→2.071 Å / Redundancy: 3.22 % / Mean I/σ(I) obs: 1.39 / Num. unique obs: 2821 / CC1/2: 0.718 / % possible all: 95.85

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Modeler

Resolution: 1.999→43.32 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2257 1470 5 %
Rwork0.1821 27904 -
obs0.1843 29374 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.27 Å2 / Biso mean: 69.956 Å2 / Biso min: 39.06 Å2
Refinement stepCycle: final / Resolution: 1.999→43.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 12 123 2753
Biso mean--89.19 62.26 -
Num. residues----335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092691
X-RAY DIFFRACTIONf_angle_d1.0013629
X-RAY DIFFRACTIONf_chiral_restr0.054376
X-RAY DIFFRACTIONf_plane_restr0.006479
X-RAY DIFFRACTIONf_dihedral_angle_d19.4181621
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1063X-RAY DIFFRACTION10.819TORSIONAL
12C1063X-RAY DIFFRACTION10.819TORSIONAL
21B411X-RAY DIFFRACTION10.819TORSIONAL
22D411X-RAY DIFFRACTION10.819TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.999-2.07010.37721400.3497264695
2.0701-2.1530.32661470.28022787100
2.153-2.2510.29341460.24772776100
2.251-2.36970.26811470.22232801100
2.3697-2.51810.25041470.20712787100
2.5181-2.71250.27121470.21482786100
2.7125-2.98540.23921470.21072804100
2.9854-3.41730.27551490.20982819100
3.4173-4.30480.20191480.16222820100
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)
14.3185-1.72842.37098.25180.77546.4061-0.42841.0770.1968-0.84550.4435-1.18560.70030.867-0.0240.70840.05380.15690.817-0.01610.690832.819114.50329.1914
24.86484.4263-6.54234.0686-6.08839.1533-0.51841.1789-0.4475-0.70660.7405-2.24880.4071-0.11770.13610.7415-0.0810.22930.7433-0.04631.012529.152933.608610.4421
34.7152-2.9343-1.13878.2296-0.49574.27310.44930.1132-0.5262-1.4449-0.4692-1.06190.6934-0.2872-0.09880.7955-0.02860.07660.55150.0610.549222.545918.35388.8614
46.3355-3.8796-1.31896.2256-0.09217.6167-0.03210.05760.1150.19940.0349-0.20490.8251-0.1413-0.06590.5433-0.05860.04780.41640.00570.411823.494617.538715.0822
54.3473-3.0318-0.05939.3761-0.89623.40890.06440.624-0.0031-0.66920.19220.30340.8999-0.3862-0.09750.6327-0.1460.00130.444-0.00830.407420.324618.90210.0814
65.6806-2.44690.39177.93321.79032.1343-0.05250.7057-0.2443-0.74480.2328-0.58730.7963-0.0938-0.13350.9562-0.14110.18630.5683-0.030.338225.059111.49935.3639
76.59322.9004-4.50943.5348-1.54212.57160.00870.152-0.8425-0.0106-0.0729-0.6515-0.04950.08290.13640.4832-0.05560.0370.46930.14070.597913.286234.266219.7004
84.4628-2.87640.56233.4393-3.07214.89030.12740.7631-1.8001-1.9858-0.00252.79350.567-1.7056-0.2240.5778-0.1419-0.09060.89620.15481.1495-16.022343.10028.6606
93.9555-0.98611.21524.82980.51053.4949-0.20040.08940.37210.0954-0.0544-0.2038-0.8918-0.45710.010.49570.1401-0.11650.71070.22650.6647-14.93559.7168.5738
106.1181-4.98043.34414.1732-2.59012.12780.9098-0.5079-1.0557-0.6519-0.67440.82930.8059-1.7318-0.11840.553-0.22650.01720.83820.08310.8303-9.483938.059417.0847
114.1101-2.01571.69936.2384-1.18734.23030.28360.6442-0.0291-0.6533-0.4239-0.373-0.0990.09830.25470.5446-0.0110.00670.62990.22810.5529-4.002851.28283.7835
123.5710.1101-0.72015.1886-0.67154.01250.1607-0.00420.17610.262-0.3056-0.5351-0.682-0.20870.17870.4113-0.0498-0.03160.50780.24580.6542-5.004854.03315.0299
132.8307-2.2750.96315.55620.26942.1780.19280.4360.0646-0.7975-0.3399-0.214-0.5017-0.1660.20630.6379-0.0179-0.01330.68230.29150.6326-7.683756.64374.5299
142.8344-3.17911.44727.6617-3.62782.49140.08380.5224-0.1054-0.5635-0.2625-0.2037-0.0330.09960.18420.5453-0.05710.01040.6130.23520.6028-3.787445.96935.9867
159.29443.5287-5.41094.1068-2.24144.81410.74190.10220.96220.2043-0.1911-0.2414-0.75260.1971-0.5470.4138-0.08830.00470.50430.16520.72319.527640.419.0335
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )A1 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 32 )A26 - 32
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 39 )A33 - 39
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 80 )A40 - 80
5X-RAY DIFFRACTION5chain 'A' and (resid 81 through 106 )A81 - 106
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 127 )A107 - 127
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 42 )B1 - 42
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 7 )C1 - 7
9X-RAY DIFFRACTION9chain 'C' and (resid 8 through 24 )C8 - 24
10X-RAY DIFFRACTION10chain 'C' and (resid 25 through 32 )C25 - 32
11X-RAY DIFFRACTION11chain 'C' and (resid 33 through 51 )C33 - 51
12X-RAY DIFFRACTION12chain 'C' and (resid 52 through 80 )C52 - 80
13X-RAY DIFFRACTION13chain 'C' and (resid 81 through 96 )C81 - 96
14X-RAY DIFFRACTION14chain 'C' and (resid 97 through 124 )C97 - 124
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 42 )D1 - 42

+
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