[English] 日本語
Yorodumi
- PDB-3qwo: Crystal structure of a motavizumab epitope-scaffold bound to mota... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qwo
TitleCrystal structure of a motavizumab epitope-scaffold bound to motavizumab Fab
Components
  • motavizumab epitope scaffold
  • motavizumab heavy chain
  • motavizumab light chain
KeywordsIMMUNE SYSTEM / Immune complex
Function / homologyImmunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Function and homology information
Biological speciesMus musculus (house mouse)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMcLellan, J.S. / Kwong, P.D.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Design and characterization of epitope-scaffold immunogens that present the motavizumab epitope from respiratory syncytial virus.
Authors: McLellan, J.S. / Correia, B.E. / Chen, M. / Yang, Y. / Graham, B.S. / Schief, W.R. / Kwong, P.D.
History
DepositionFeb 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: motavizumab light chain
H: motavizumab heavy chain
B: motavizumab light chain
A: motavizumab heavy chain
C: motavizumab epitope scaffold
P: motavizumab epitope scaffold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,85412
Polymers107,3806
Non-polymers4746
Water9,170509
1
L: motavizumab light chain
H: motavizumab heavy chain
P: motavizumab epitope scaffold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9446
Polymers53,6903
Non-polymers2543
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: motavizumab light chain
A: motavizumab heavy chain
C: motavizumab epitope scaffold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9106
Polymers53,6903
Non-polymers2203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.762, 74.425, 86.398
Angle α, β, γ (deg.)90.00, 101.75, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules CP

#3: Protein motavizumab epitope scaffold


Mass: 6254.640 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: homo sapiens (human)

-
Antibody , 2 types, 4 molecules LBHA

#1: Antibody motavizumab light chain


Mass: 23150.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: humanized-mouse antibody / Production host: homo sapiens (human)
#2: Antibody motavizumab heavy chain


Mass: 24284.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: humanized-mouse antibody / Production host: homo sapiens (human)

-
Non-polymers , 3 types, 515 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20.5% (w/v) PEG 4000, 0.2 M lithium sulfate monohydrate, 0.1 M Tris-HCl pH 8.5, 100 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 10, 2010
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 73584 / Num. obs: 73143 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2 / % possible all: 92

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3IXT, 1LP1

3ixt

1lp1


Resolution: 1.9→36.836 Å / SU ML: 0.26 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 3589 5.13 %random
Rwork0.1875 ---
all0.1897 73697 --
obs0.1897 69917 94.87 %-
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.051 Å2 / ksol: 0.401 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6225 Å20 Å23.4157 Å2
2--4.0244 Å2-0 Å2
3----0.4018 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7362 0 27 509 7898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077559
X-RAY DIFFRACTIONf_angle_d1.03410270
X-RAY DIFFRACTIONf_dihedral_angle_d11.5862711
X-RAY DIFFRACTIONf_chiral_restr0.0671170
X-RAY DIFFRACTIONf_plane_restr0.0051310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92930.3321020.26241932X-RAY DIFFRACTION73
1.9293-1.95580.25591220.22862187X-RAY DIFFRACTION82
1.9558-1.98370.23071220.21772274X-RAY DIFFRACTION86
1.9837-2.01330.25011300.22062472X-RAY DIFFRACTION90
2.0133-2.04480.27541310.21162422X-RAY DIFFRACTION91
2.0448-2.07830.26981370.20192460X-RAY DIFFRACTION92
2.0783-2.11410.24561460.19912489X-RAY DIFFRACTION93
2.1141-2.15260.22831580.18562490X-RAY DIFFRACTION94
2.1526-2.1940.25221340.17992526X-RAY DIFFRACTION95
2.194-2.23870.2041300.18522540X-RAY DIFFRACTION95
2.2387-2.28740.24151300.18132595X-RAY DIFFRACTION96
2.2874-2.34060.26491470.19252560X-RAY DIFFRACTION96
2.3406-2.39910.25181430.19912603X-RAY DIFFRACTION97
2.3991-2.4640.24331480.19192600X-RAY DIFFRACTION97
2.464-2.53650.26461400.19432662X-RAY DIFFRACTION98
2.5365-2.61830.22391480.19832610X-RAY DIFFRACTION98
2.6183-2.71190.27141380.19462640X-RAY DIFFRACTION98
2.7119-2.82040.23241290.19472681X-RAY DIFFRACTION99
2.8204-2.94870.2661470.19612654X-RAY DIFFRACTION99
2.9487-3.10410.2481240.19812707X-RAY DIFFRACTION99
3.1041-3.29850.25951400.19042678X-RAY DIFFRACTION100
3.2985-3.5530.22481450.18352699X-RAY DIFFRACTION100
3.553-3.91020.2111390.17582703X-RAY DIFFRACTION100
3.9102-4.47510.1751530.15182699X-RAY DIFFRACTION100
4.4751-5.6350.21141580.16452718X-RAY DIFFRACTION100
5.635-36.84330.22561480.21012727X-RAY DIFFRACTION98
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)
11.4565-1.3467-0.30252.12370.17040.5809-0.09380.0548-0.0934-0.00980.142-0.3630.22790.0174-0.04580.2417-0.00040.03120.1778-0.0590.2689-4.7182-21.843923.8324
22.678-0.1923-0.19030.91640.48280.8672-0.2539-1.2742-0.37880.0273-0.0118-0.2574-0.01330.14330.21530.11830.0555-0.07260.6887-0.04140.633316.5395-11.35152.3211
32.0569-1.0441-0.1061.11320.85321.6472-0.02980.0308-0.07260.08680.2269-0.04790.32820.2064-0.16140.24020.0448-0.03850.1877-0.02230.15795.0541-20.7995-18.4438
40.6554-0.47690.17880.7250.23730.9933-0.03880.134-0.1460.0299-0.04810.0660.01660.40260.03390.1734-0.0002-0.03230.4962-0.13130.337524.8725-10.627510.6421
51.38840.5487-0.28040.43960.39092.08590.01750.1010.06660.06690.1112-0.0153-0.1738-0.1701-0.12620.17970.01480.01820.15640.04130.1409-18.4848-5.922331.4524
61.6331-0.3966-1.17711.8711-0.36692.44070.3963-0.23260.5995-0.0943-0.0221-0.8213-0.23440.5933-0.35740.1132-0.07950.08310.1627-0.15810.48759.43990.814244.568
71.04630.19770.3670.35160.6272.14520.1-0.04820.15070.04830.01390.01010.0306-0.1894-0.11570.160.00470.01920.16850.02950.1391-10.0022-5.9206-10.8137
80.79-0.4241.17152.9462-0.60592.80040.10650.4360.38050.013-0.2582-0.6548-0.42410.7740.19750.2346-0.1304-0.01010.41980.04280.47117.62121.86873.5202
90.45330.0733-0.40570.42240.031.4169-0.12230.92420.0658-0.07370.09880.07680.0453-0.6718-0.01510.1786-0.0544-0.00410.74960.05870.2217-29.23-10.90377.2717
100.4895-0.35270.16421.1630.28072.11680.06150.3092-0.0709-0.0833-0.09990.1899-0.0658-0.64180.0040.16850.0268-0.02770.39460.02430.2165-19.8428-11.4522-35.2561
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain L and resid 1:109
2X-RAY DIFFRACTION2chain L and resid 110:212
3X-RAY DIFFRACTION3chain B and resid 1:109
4X-RAY DIFFRACTION4chain B and resid 110:212
5X-RAY DIFFRACTION5chain H and resid 1:114
6X-RAY DIFFRACTION6chain H and resid 115:213
7X-RAY DIFFRACTION7chain A and resid 1:114
8X-RAY DIFFRACTION8chain A and resid 115:213
9X-RAY DIFFRACTION9chain P
10X-RAY DIFFRACTION10chain C

+
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