[English] 日本語
Yorodumi
- PDB-3hmw: Crystal structure of ustekinumab FAB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hmw
TitleCrystal structure of ustekinumab FAB
Components
  • USTEKINUMAB FAB HEAVY CHAIN
  • USTEKINUMAB FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / USTEKINUMAB / CNTO1275 / IL-12 / IL-23 / ANTIBODY / FAB / MONOCLONAL ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLuo, J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural basis for the dual recognition of IL-12 and IL-23 by ustekinumab.
Authors: Luo, J. / Wu, S.J. / Lacy, E.R. / Orlovsky, Y. / Baker, A. / Teplyakov, A. / Obmolova, G. / Heavner, G.A. / Richter, H.T. / Benson, J.
History
DepositionMay 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 22, 2015Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: USTEKINUMAB FAB LIGHT CHAIN
H: USTEKINUMAB FAB HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0614
Polymers47,8362
Non-polymers2252
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-24 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.310, 139.310, 114.580
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11L-215-

CD

21L-216-

CD

31L-229-

HOH

41L-231-

HOH

-
Components

#1: Antibody USTEKINUMAB FAB LIGHT CHAIN


Mass: 23474.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: PAPAIN DIGESTED FROM mAb / Cell line (production host): HEK 293 / Production host: HOMO SAPIENS (human)
#2: Antibody USTEKINUMAB FAB HEAVY CHAIN


Mass: 24361.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: PAPAIN DIGESTED FROM mAb / Cell line (production host): HEK 293 / Production host: HOMO SAPIENS (human)
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 3.35 Å3/Da / Density % sol: 63.34 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→69.65 Å / Num. all: 13596 / Num. obs: 13596 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 40 % / Biso Wilson estimate: 58.35 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 25.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 38.5 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 9 / Num. unique all: 1318 / % possible all: 98.7

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→34.827 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.88 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.287 673 5.05 %
Rwork0.228 --
obs0.231 13324 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.577 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 137.31 Å2 / Biso mean: 52.532 Å2 / Biso min: 3.27 Å2
Baniso -1Baniso -2Baniso -3
1--3.765 Å20 Å20 Å2
2---3.765 Å20 Å2
3---4.579 Å2
Refinement stepCycle: LAST / Resolution: 3→34.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 2 125 3426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033383
X-RAY DIFFRACTIONf_angle_d0.7574594
X-RAY DIFFRACTIONf_chiral_restr0.05512
X-RAY DIFFRACTIONf_plane_restr0.003584
X-RAY DIFFRACTIONf_dihedral_angle_d17.7231192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.2320.4181430.312466260998
3.232-3.5560.3831400.2762451259197
3.556-4.070.2891120.2222507261998
4.07-5.1260.2191310.1742521265297
5.126-34.830.2271470.2192706285398
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.5666-1.1814-0.01870.6024-0.82672.041-0.0042-0.1708-0.31410.0826-0.08010.2669-0.13050.11510.07620.3084-0.067-0.02530.22850.03030.351265.6786-18.26363.522
21.34820.81760.25013.2713-1.00431.456-0.0465-0.23390.1538-0.16790.0984-0.52750.05320.0471-0.05270.27480.0143-0.04130.3003-0.05680.4812103.2411-13.5851.2215
31.92990.0607-0.3686-0.27-1.36893.0503-0.04650.0245-0.01860.1911-0.0442-0.0262-0.4094-0.20840.09760.38750.0429-0.06760.2624-0.03410.384265.6015-10.3771-17.1215
42.9033-0.00170.7322.5305-1.9291.2709-0.05050.26650.0084-0.49690.0517-0.0290.23590.0908-0.01810.6377-0.11860.0010.3326-0.01130.361897.1037-18.1626-12.9985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain L and resid 1:109)L1 - 109
2X-RAY DIFFRACTION2(chain L and resid 110:214)L110 - 214
3X-RAY DIFFRACTION3(chain H and resid 1:119)H1 - 119
4X-RAY DIFFRACTION4(chain H and resid 120:223)H120 - 223

+
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