[English] 日本語
Yorodumi
- PDB-7q1s: A de novo designed hetero-dimeric antiparallel coiled coil apCC-D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q1s
TitleA de novo designed hetero-dimeric antiparallel coiled coil apCC-Di-AB_var
Components
  • apCC-Di-A_var
  • apCC-Di-B_var
KeywordsDE NOVO PROTEIN / antiparallel / hetero-dimeric / coiled-coil / de novo / protein design / associating peptides
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsShanmugaratnam, S. / Rhys, G.G. / Dawson, W.M. / Woolfson, D.N. / Hocker, B.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission888993European Union
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: De novo designed peptides for cellular delivery and subcellular localisation.
Authors: Rhys, G.G. / Cross, J.A. / Dawson, W.M. / Thompson, H.F. / Shanmugaratnam, S. / Savery, N.J. / Dodding, M.P. / Hocker, B. / Woolfson, D.N.
History
DepositionOct 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: apCC-Di-B_var
E: apCC-Di-A_var
L: apCC-Di-B_var
K: apCC-Di-A_var
I: apCC-Di-A_var
J: apCC-Di-B_var
D: apCC-Di-B_var
C: apCC-Di-A_var
M: apCC-Di-A_var
N: apCC-Di-B_var
H: apCC-Di-B_var
G: apCC-Di-A_var
A: apCC-Di-A_var
B: apCC-Di-B_var
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,17519
Polymers47,86514
Non-polymers3105
Water2,450136
1
F: apCC-Di-B_var
E: apCC-Di-A_var
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9624
Polymers6,8382
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-11 kcal/mol
Surface area5060 Å2
MethodPISA
2
L: apCC-Di-B_var
K: apCC-Di-A_var


Theoretical massNumber of molelcules
Total (without water)6,8382
Polymers6,8382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-12 kcal/mol
Surface area4790 Å2
MethodPISA
3
I: apCC-Di-A_var
J: apCC-Di-B_var


Theoretical massNumber of molelcules
Total (without water)6,8382
Polymers6,8382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-12 kcal/mol
Surface area4720 Å2
MethodPISA
4
D: apCC-Di-B_var
C: apCC-Di-A_var
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9003
Polymers6,8382
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-13 kcal/mol
Surface area5100 Å2
MethodPISA
5
M: apCC-Di-A_var
N: apCC-Di-B_var
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9003
Polymers6,8382
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-14 kcal/mol
Surface area4580 Å2
MethodPISA
6
H: apCC-Di-B_var
G: apCC-Di-A_var
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9003
Polymers6,8382
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-12 kcal/mol
Surface area4580 Å2
MethodPISA
7
A: apCC-Di-A_var
B: apCC-Di-B_var


Theoretical massNumber of molelcules
Total (without water)6,8382
Polymers6,8382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-14 kcal/mol
Surface area4700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.196, 62.457, 64.557
Angle α, β, γ (deg.)90.000, 111.210, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide
apCC-Di-B_var


Mass: 3461.121 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide
apCC-Di-A_var


Mass: 3376.683 Da / Num. of mol.: 7 / 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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Magnesium acetate pH6.5, 20% PEG 8000, 0.1M Sodium cacodylate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 28, 2021
RadiationMonochromator: DCM (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.99→55.19 Å / Num. obs: 29353 / % possible obs: 95.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 37.2 Å2 / CC1/2: 0.973 / CC star: 0.993 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.076 / Rrim(I) all: 0.148 / Net I/σ(I): 13.19
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.445 / Mean I/σ(I) obs: 0.84 / Num. unique obs: 2857 / CC1/2: 0.197 / CC star: 0.574 / Rpim(I) all: 0.886 / Rrim(I) all: 1.704 / % possible all: 84.6

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
DIALS2.0.2data reduction
DIALS2.0.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: poly-alanine coiled-coil

Resolution: 1.99→55.19 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 1977 6.86 %
Rwork0.1951 26858 -
obs0.1984 28834 95.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.98 Å2 / Biso mean: 49.8 Å2 / Biso min: 18.32 Å2
Refinement stepCycle: final / Resolution: 1.99→55.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 50 136 3474
Biso mean--71.51 48.37 -
Num. residues----411
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.99-2.040.40131220.3835162981
2.04-2.10.39091380.3179188295
2.1-2.160.34071430.2714194198
2.16-2.230.26651450.218196498
2.23-2.310.27111440.2114195898
2.31-2.40.25281330.2141180591
2.4-2.510.26531440.1972197399
2.51-2.640.25951440.1906194599
2.64-2.810.28051480.1966201799
2.81-3.030.25481420.1832193598
3.03-3.330.24511450.1954197497
3.33-3.810.20051360.1561185093
3.81-4.80.18661480.1661200998
4.8-55.190.24811450.2035197695
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)
12.8321-0.7611-0.40611.60510.1490.91340.0386-0.14370.0795-0.060.06840.0469-0.00130.576400.3287-0.09-0.01260.309-0.03160.351213.75428.298417.6318
23.24360.18620.08723.2927-2.41992.7079-0.0577-0.00850.2113-0.0430.09160.20560.02360.3618-00.2408-0.0856-0.05280.31760.09840.41646.511210.16912.9115
32.9473-1.29510.16832.7035-0.32586.68340.0348-0.01250.31510.5011-0.15530.5686-0.0320.03820.00070.26670.0962-0.02010.2652-0.00640.145613.942615.4106-11.3838
41.7775-0.316-1.91922.2316-1.9676.74960.01350.2241-0.0619-0.0761-0.09950.11940.02280.2019-0.00160.26170.09720.0320.2570.03540.282717.472714.0067-19.0258
53.9332-2.28640.90742.89881.38946.4243-0.217-0.1783-0.05680.12780.1614-0.0571-0.09570.0322-0.00010.24750.1086-0.03050.2859-0.05350.22317.956121.3228-11.5076
63.0162-1.77432.36763.1619-0.65215.24860.50191.1047-0.13110.2065-0.10050.0849-0.2577-0.60890.06110.28540.1265-0.06250.1667-0.0790.25685.51123.9896-19.6662
71.7947-0.5937-1.87522.7099-0.00782.00270.3911-0.11930.06950.1191-0.15820.1896-0.0465-0.448100.3695-0.15780.11020.4046-0.01870.384816.34322.70315.2828
82.4345-2.37471.02783.9303-0.20560.7143-0.10390.1066-0.02450.284-0.03410.2143-0.07760.1057-0.00190.2766-0.13690.02390.29190.01620.361119.644914.667216.0657
93.9342-0.8961-0.97763.705-3.1045.61580.04830.3840.14960.83370.22680.45680.55690.44420.00730.32450.11930.09750.26050.02910.247322.84482.1075-12.9266
103.3978-1.5194-1.48922.0691-1.31985.78750.0081-0.20210.02880.1995-0.01860.0206-0.1160.2921-0.00150.25060.1008-0.01160.2587-0.00120.215724.00777.8093-18.9932
113.07971.20551.39193.4239-2.06453.1036-0.01360.01420.2422-0.68230.1472-0.1776-0.29480.39170.00940.2088-0.0762-0.07540.25870.01920.39380.70693.727212.3315
123.23411.76531.69763.0393-1.87555.07570.2943-0.225-0.0727-0.1472-0.0489-0.3941-0.15830.23260.00540.2341-0.1346-0.05640.22740.05750.3020.7349-1.51418.781
134.29930.3921-1.81895.34942.03541.9111-0.29060.0470.3429-0.209-0.2499-0.31430.5324-0.9706-0.09320.2928-0.21170.04350.4164-0.0390.35122.811728.786116.3949
144.37940.7603-2.21923.04152.36113.708-0.60380.403-0.0454-0.18210.0023-0.61270.905-0.6694-0.05530.4186-0.17390.06530.333-0.07490.317330.252326.714912.7934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 30)A0 - 30
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 29)B1 - 29
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 29)C1 - 29
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 28)D2 - 28
5X-RAY DIFFRACTION5(chain 'E' and resid 2 through 29)E2 - 29
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 30)F1 - 30
7X-RAY DIFFRACTION7(chain 'G' and resid 2 through 29)G2 - 29
8X-RAY DIFFRACTION8(chain 'H' and resid 2 through 29)H2 - 29
9X-RAY DIFFRACTION9(chain 'I' and resid 2 through 29)I2 - 29
10X-RAY DIFFRACTION10(chain 'J' and resid 1 through 30)J1 - 30
11X-RAY DIFFRACTION11(chain 'K' and resid 2 through 28)K2 - 28
12X-RAY DIFFRACTION12(chain 'L' and resid 2 through 29)L2 - 29
13X-RAY DIFFRACTION13(chain 'M' and resid 1 through 30)M1 - 30
14X-RAY DIFFRACTION14(chain 'N' and resid 1 through 29)N1 - 29

+
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://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