[English] 日本語
Yorodumi
- PDB-6au5: Structure of cetuximab with aminoheptanoic acid-linked n-butylarg... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6au5
TitleStructure of cetuximab with aminoheptanoic acid-linked n-butylarginine meditope variant
Components
  • cetuximab Fab heavy chain
  • cetuximab Fab light chain
  • meditope
KeywordsIMMUNE SYSTEM / antibody / anti-EGFR
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / IgG H chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.484 Å
AuthorsBzymek, K.P. / Williams, J.C.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Meditope-Fab interaction: threading the hole.
Authors: Bzymek, K.P. / Ma, Y. / Avery, K.N. / Horne, D.A. / Williams, J.C.
History
DepositionAug 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cetuximab Fab light chain
B: cetuximab Fab heavy chain
C: cetuximab Fab light chain
D: cetuximab Fab heavy chain
E: meditope
F: meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1849
Polymers96,8966
Non-polymers2883
Water5,296294
1
A: cetuximab Fab light chain
B: cetuximab Fab heavy chain
E: meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5444
Polymers48,4483
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-41 kcal/mol
Surface area18660 Å2
MethodPISA
2
C: cetuximab Fab light chain
D: cetuximab Fab heavy chain
F: meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6405
Polymers48,4483
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-49 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.580, 83.060, 211.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody cetuximab Fab light chain


Mass: 23287.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: purified from commercial cetuximab IgG (erbitux)
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: IGKC / Production host: unidentified (others) / References: UniProt: P01834
#2: Antibody cetuximab Fab heavy chain


Mass: 23725.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: purified from commercial cetuximab IgG (erbitux)
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: unidentified (others) / References: UniProt: S6B291
#3: Protein/peptide meditope


Mass: 1434.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Source detailscetuximab Fab light chain in this entry matches to the sequence from the first deposited cetuximab ...cetuximab Fab light chain in this entry matches to the sequence from the first deposited cetuximab structure in PDB (1yy8).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate, pH 4.0, 1.6 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.48→33.173 Å / Num. obs: 40278 / % possible obs: 98 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Net I/σ(I): 34.8
Reflection shellResolution: 2.48→2.55 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 9.2 / Num. unique obs: 2533 / CC1/2: 0.973 / % possible all: 85

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ID0

5id0


Resolution: 2.484→33.173 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.43
RfactorNum. reflection% reflection
Rfree0.2265 2014 5 %
Rwork0.1858 --
obs0.1878 40272 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.484→33.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6755 0 15 294 7064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056938
X-RAY DIFFRACTIONf_angle_d1.0239451
X-RAY DIFFRACTIONf_dihedral_angle_d10.0524131
X-RAY DIFFRACTIONf_chiral_restr0.0651068
X-RAY DIFFRACTIONf_plane_restr0.0041204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.484-2.54610.25371210.20922302X-RAY DIFFRACTION84
2.5461-2.61490.26631420.20932695X-RAY DIFFRACTION98
2.6149-2.69190.2841430.21122726X-RAY DIFFRACTION99
2.6919-2.77870.30071420.21692705X-RAY DIFFRACTION99
2.7787-2.8780.26111430.20982704X-RAY DIFFRACTION99
2.878-2.99310.27721440.19722733X-RAY DIFFRACTION99
2.9931-3.12920.25821430.20272725X-RAY DIFFRACTION99
3.1292-3.29410.23451450.19872748X-RAY DIFFRACTION99
3.2941-3.50030.22251450.18182759X-RAY DIFFRACTION99
3.5003-3.77020.2291460.17482784X-RAY DIFFRACTION99
3.7702-4.14890.2121460.16272774X-RAY DIFFRACTION99
4.1489-4.74780.16471470.14072788X-RAY DIFFRACTION99
4.7478-5.9760.17771500.16762852X-RAY DIFFRACTION100
5.976-33.17610.24791570.22652963X-RAY DIFFRACTION99
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)
12.7562-1.72091.33592.4122-3.50056.06320.37240.467-0.3263-0.1279-0.09190.37630.4017-0.1637-0.29270.4813-0.1278-0.0780.4786-0.12080.3408-12.682323.856919.2263
20.7304-0.0982-1.02310.56970.36081.59350.36460.4101-0.2073-0.41540.15990.27640.20660.2559-0.40040.4137-0.0225-0.03320.5728-0.15310.2337-8.218430.604610.6672
31.85530.2522-0.53173.6888-1.71282.3535-0.00650.2126-0.3539-0.18370.056-0.08390.3914-0.1176-0.05350.4510.024-0.10220.4468-0.15680.3041-4.121127.113415.4837
40.0796-0.33110.49391.9546-3.30965.85240.0787-0.0278-0.0338-0.520.20780.009-0.02550.1685-0.23640.37290.0116-0.10430.2597-0.10040.3453-6.944917.968236.2031
53.66490.94830.50421.2963-1.27412.72140.0608-0.3190.26820.556-0.003-0.4525-0.35980.3274-0.07410.2383-0.0676-0.03780.2994-0.08350.32572.525637.382357.7249
61.7458-1.0477-0.39376.87546.5436.6072-0.0550.164-0.1338-0.12040.1346-0.03070.1511-0.24250.15390.17460.019-0.07980.117-0.05420.3643-7.249427.853550.4652
74.6465-0.5982-5.09680.80762.32029.34940.00410.0005-0.36720.01590.00530.03660.654-0.0894-0.00660.23870.0096-0.06290.2696-0.03720.3458-12.268534.259255.3655
82.14750.2805-0.6292.75542.06015.66170.012-0.1091-0.1993-0.0683-0.05570.1028-0.21260.06450.07380.11870.027-0.03240.1725-0.02020.2966-5.590928.915454.5849
94.8573-2.4881-3.42133.3722.50986.5943-0.2387-0.0904-0.0470.18710.2576-0.0015-0.1150.3604-0.24280.35470.016-0.0190.4394-0.04830.28216.442948.451519.8834
105.46413.5558-5.37194.8541-4.32455.87720.1430.44030.2940.31070.35980.1413-0.3409-0.5681-0.26020.35950.0696-0.02360.4447-0.09120.1955-4.918244.327917.2907
115.31270.914-0.07172.6651-0.53672.240.11410.54690.0246-0.1330.01020.1146-0.9161-0.4417-0.1730.47330.13190.05940.6-0.0040.2504-1.812452.679110.5571
122.94030.4216-1.28852.85390.36085.9250.10040.29660.30370.0120.32770.019-0.27020.0381-0.35250.2890.0748-0.02370.4304-0.02030.24311.154547.171716.1259
131.484-0.56310.67561.70880.07294.0494-0.08980.0543-0.0783-0.00470.041-0.0745-0.2855-0.14380.00130.1013-0.01310.00860.1724-0.03470.28923.107439.22241.9249
142.1233-1.23620.30753.6745-1.46811.4385-0.07660.0917-0.0571-0.08120.07920.0271-0.0102-0.02970.01180.17640.0118-0.03360.2296-0.1370.24484.085936.116343.2964
158.5246-7.30584.56848.9228-7.97658.8242-0.12560.60280.03820.0941-0.3148-0.6448-0.1420.49130.49750.2005-0.0406-0.0570.1915-0.01890.239512.968838.240545.0824
164.9556-1.51381.74634.5968-4.76345.29150.10990.20380.0750.9272-0.2242-0.13-0.95520.59350.02240.2615-0.0394-0.07010.2111-0.00160.356312.742340.730949.9917
170.28920.47950.84441.23052.55035.7232-0.09420.31750.1792-0.32630.3176-0.0323-0.45310.3598-0.22770.4202-0.08490.0210.38790.07920.3283-26.266614.617316.3002
182.3004-0.9331.28562.9754-2.46014.1297-0.0886-0.15140.13380.13520.0945-0.087-0.0823-0.14960.01470.1490.02710.00040.1507-0.01050.2449-26.72667.841452.5142
192.3101-1.50822.40195.7747-4.10874.0218-0.1288-0.2060.3491-0.15360.3126-0.7510.763-0.4502-0.3160.4110.0405-0.07250.5166-0.09910.3963-35.261-10.280222.8814
202.3361-0.29920.05092.29320.09071.5625-0.46350.5057-0.2108-0.07980.40190.0595-0.0425-0.18980.14480.5047-0.1048-0.0140.4433-0.03160.2412-36.0292-4.963813.6727
213.17610.78681.15893.29371.13814.4805-0.05380.3769-0.4986-0.07680.3426-0.15080.51930.178-0.28120.4387-0.0282-0.00340.4243-0.04140.2468-32.4142-10.49879.913
221.9298-0.02250.83230.5254-0.06675.0084-0.16910.5078-0.0631-0.07430.0418-0.08580.34960.17370.06470.4213-0.02090.0010.3712-0.04420.2337-31.8169-3.28915.7351
233.7944-0.6664-3.40511.33291.03937.0566-0.52450.1503-0.67780.5547-0.01460.11790.96050.06190.32140.23280.0002-0.01010.12950.00420.2795-33.9429-8.581543.9009
247.0484-1.50223.21890.3394-0.75771.7056-0.8423-0.74281.58591.34760.6262-1.50430.27960.27380.10940.82450.1515-0.15140.57-0.28280.7619-38.691114.289756.3391
250.5648-0.6683-1.19265.26354.36274.4817-0.1339-0.0374-0.3018-0.12420.33250.26390.22610.2699-0.12420.20510.0248-0.04460.19140.08420.2644-34.6581-1.570443.0149
266.97361.6297-0.05122.84290.8433.0657-0.30240.35710.373-0.66410.25210.3313-0.5295-0.27060.12010.26420.0004-0.04530.22870.07660.1878-43.1626.872739.5383
270.4668-1.2313-0.30934.54860.35832.2494-0.1548-0.2963-0.01370.24910.1438-0.2370.1539-0.06660.01190.1243-0.0108-0.040.16370.03840.1994-36.60933.874345.4972
288.5049-6.6054-3.98055.1533.39923.22960.28510.6073-0.4117-0.2439-0.17250.09810.2144-0.211-0.05240.2693-0.0221-0.06550.14130.01380.2761-42.4666-3.612839.8455
293.2534-1.8948-2.24024.37834.93735.58870.040.02780.01720.38990.1395-0.17510.4936-0.3328-0.15840.2459-0.053-0.00850.18110.04690.3332-45.0412-2.375447.9539
308.02885.2404-2.08565.0275-2.7592.63240.39230.07340.0671.1373-0.07680.3270.1573-1.06040.09290.3960.07-0.00590.6603-0.2210.3268-7.026236.284630.5742
315.70453.6648-5.23213.4041-2.25085.99610.34590.0848-0.75531.2421-0.30920.08850.26690.73490.0490.3617-0.0105-0.06790.4993-0.01310.3892-25.64293.558328.5391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:25)
2X-RAY DIFFRACTION2chain 'A' and (resseq 26:38)
3X-RAY DIFFRACTION3chain 'A' and (resseq 39:102)
4X-RAY DIFFRACTION4chain 'A' and (resseq 103:113)
5X-RAY DIFFRACTION5chain 'A' and (resseq 114:128)
6X-RAY DIFFRACTION6chain 'A' and (resseq 129:150)
7X-RAY DIFFRACTION7chain 'A' and (resseq 151:163)
8X-RAY DIFFRACTION8chain 'A' and (resseq 164:212)
9X-RAY DIFFRACTION9chain 'B' and (resseq 1:33)
10X-RAY DIFFRACTION10chain 'B' and (resseq 34:51)
11X-RAY DIFFRACTION11chain 'B' and (resseq 52:72)
12X-RAY DIFFRACTION12chain 'B' and (resseq 73:105)
13X-RAY DIFFRACTION13chain 'B' and (resseq 106:151)
14X-RAY DIFFRACTION14chain 'B' and (resseq 152:194)
15X-RAY DIFFRACTION15chain 'B' and (resseq 195:209)
16X-RAY DIFFRACTION16chain 'B' and (resseq 210:221)
17X-RAY DIFFRACTION17chain 'C' and (resseq 1:113)
18X-RAY DIFFRACTION18chain 'C' and (resseq 114:213)
19X-RAY DIFFRACTION19chain 'D' and (resseq 1:17)
20X-RAY DIFFRACTION20chain 'D' and (resseq 18:43)
21X-RAY DIFFRACTION21chain 'D' and (resseq 44:82)
22X-RAY DIFFRACTION22chain 'D' and (resseq 83:117)
23X-RAY DIFFRACTION23chain 'D' and (resseq 118:131)
24X-RAY DIFFRACTION24chain 'D' and (resseq 132:140)
25X-RAY DIFFRACTION25chain 'D' and (resseq 141:156)
26X-RAY DIFFRACTION26chain 'D' and (resseq 157:171)
27X-RAY DIFFRACTION27chain 'D' and (resseq 172:199)
28X-RAY DIFFRACTION28chain 'D' and (resseq 200:209)
29X-RAY DIFFRACTION29chain 'D' and (resseq 210:220)
30X-RAY DIFFRACTION30chain 'E' and (resseq 2:11)
31X-RAY DIFFRACTION31chain 'F' and (resseq 2:11)

+
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