[English] 日本語
Yorodumi
- PDB-5ea0: Structure of the antibody 7968 with human complement factor H-der... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ea0
TitleStructure of the antibody 7968 with human complement factor H-derived peptide
Components
  • Complement factor H-related protein 2
  • Heavy chain of antibody 7968 Fab fragment
  • Light chain of antibody 7968 Fab fragment
KeywordsIMMUNE SYSTEM / complement factor H CFH SCR19 SCR19-20
Function / homology
Function and homology information


complement component C3b binding / complement activation / cytolysis by host of symbiont cells / negative regulation of protein binding / Regulation of Complement cascade / protein-containing complex / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Complement factor H-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBushey, R.T. / Moody, M.A. / Nicely, N.I. / Alam, S.M. / Haynes, B.F. / Winkler, M.T. / Gottlin, E.B. / Campa, M.J. / Liao, H.-X. / Patz Jr., E.F.
CitationJournal: Cell Rep / Year: 2016
Title: A Therapeutic Antibody for Cancer, Derived from Single Human B Cells.
Authors: Bushey, R.T. / Moody, M.A. / Nicely, N.L. / Haynes, B.F. / Alam, S.M. / Keir, S.T. / Bentley, R.C. / Roy Choudhury, K. / Gottlin, E.B. / Campa, M.J. / Liao, H.X. / Patz, E.F.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Mar 24, 2021Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_host_org_strain / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Heavy chain of antibody 7968 Fab fragment
L: Light chain of antibody 7968 Fab fragment
P: Complement factor H-related protein 2


Theoretical massNumber of molelcules
Total (without water)49,3553
Polymers49,3553
Non-polymers00
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-34 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.280, 65.547, 71.267
Angle α, β, γ (deg.)90.00, 106.37, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody Heavy chain of antibody 7968 Fab fragment


Mass: 23648.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody Light chain of antibody 7968 Fab fragment


Mass: 24403.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Protein/peptide Complement factor H-related protein 2 / FHR-2 / DDESK59 / H factor-like 3 / H factor-like protein 2


Mass: 1303.399 Da / Num. of mol.: 1 / Fragment: UNP residues 150-162 / Source method: obtained synthetically
Details: The peptide was N-terminally acetylated and C-terminally amidated.
Source: (synth.) Homo sapiens (human) / References: UniProt: P36980
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: Drop composed of Fab at 20 mg/ml mixed with 25 mM citric acid pH 3.5, 8% PEG 3350; over a reservoir of 24% PEG 3350

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 28263 / % possible obs: 91.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 20.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.2 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NL0, 3QOS

1nl0

3qos
PDB Unreleased entry


Resolution: 2→38.009 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2753 1918 7.19 %Random selection
Rwork0.1959 ---
obs0.2017 26663 86.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→38.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3380 0 0 341 3721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093464
X-RAY DIFFRACTIONf_angle_d1.2564707
X-RAY DIFFRACTIONf_dihedral_angle_d14.8851246
X-RAY DIFFRACTIONf_chiral_restr0.045525
X-RAY DIFFRACTIONf_plane_restr0.006605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04820.37471430.24771685X-RAY DIFFRACTION83
2.0482-2.10360.31261400.23431779X-RAY DIFFRACTION88
2.1036-2.16550.30861470.22981860X-RAY DIFFRACTION92
2.1655-2.23540.408810.26671122X-RAY DIFFRACTION54
2.2354-2.31530.5329860.37681039X-RAY DIFFRACTION52
2.3153-2.4080.31261530.24021923X-RAY DIFFRACTION96
2.408-2.51750.30961540.22011964X-RAY DIFFRACTION96
2.5175-2.65020.33141500.21371964X-RAY DIFFRACTION96
2.6502-2.81620.28791430.22122024X-RAY DIFFRACTION98
2.8162-3.03360.30211550.21322025X-RAY DIFFRACTION99
3.0336-3.33870.27741630.19252033X-RAY DIFFRACTION100
3.3387-3.82140.24081140.17271489X-RAY DIFFRACTION72
3.8214-4.81310.18551290.13011728X-RAY DIFFRACTION84
4.8131-38.01630.17961600.13572110X-RAY DIFFRACTION100
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)
17.6856-4.21522.51184.4929-1.78491.03290.12760.1349-0.13830.0056-0.19540.12870.13950.0878-0.0040.2024-0.01980.0080.2024-0.00380.1106-27.7564-16.7244-6.6235
21.1091-0.4010.43710.94970.04530.7522-0.0507-0.006-0.06460.19630.0002-0.03070.0255-0.04590.03550.1492-0.00380.00420.14580.0140.1711-26.2042-9.56350.286
30.8593-0.1499-0.00530.5462-0.04080.59830.00970.0331-0.0533-0.0946-0.0056-0.05810.09730.019-0.01210.16580.02220.02410.1297-0.01680.1779-34.0224-13.2124-28.7306
41.6703-0.4637-0.74872.26971.04241.1805-0.01620.3087-0.1103-0.1780.038-0.05110.3865-0.2354-0.04490.23060.00460.00170.2238-0.02150.1509-35.9884-22.1789-29.3839
50.6087-0.1728-0.74591.05921.43544.90450.08840.04330.02720.05010.0948-0.0836-0.11530.03-0.25770.2019-0.01110.00430.18340.02340.1778-7.98584.2336-12.7651
60.8642-0.1402-0.47220.8190.08180.91130.0385-0.0827-0.0089-0.01540.0499-0.12710.06410.0339-0.0780.1447-0.0135-0.00780.17570.01320.1734-7.7302-4.4062-8.6246
71.2848-0.2990.52970.1739-0.07281.03950.01990.054-0.0452-0.0052-0.0252-0.03790.07130.0160.00980.15240.00690.00630.1245-0.00040.1469-29.9497-3.7596-36.4731
82.78470.23560.12161.0444-0.11481.2150.00150.19380.093-0.2351-0.0730.13840.0869-0.07620.04510.2143-0.0145-0.02430.1741-0.00420.1764-37.8464-2.6904-43.9985
92.22313.48010.26475.49710.58690.6146-0.0198-0.14520.00880.2352-0.0383-0.0545-0.07350.00140.05240.2623-0.0228-0.06190.2849-0.03110.1873-10.3441-7.509610.1487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 1:12)
2X-RAY DIFFRACTION2(chain H and resid 13:116)
3X-RAY DIFFRACTION3(chain H and resid 117:190)
4X-RAY DIFFRACTION4(chain H and resid 191:216)
5X-RAY DIFFRACTION5(chain L and resid 1:27A)
6X-RAY DIFFRACTION6(chain L and resid 27B:105)
7X-RAY DIFFRACTION7(chain L and resid 106:175)
8X-RAY DIFFRACTION8(chain L and resid 176:213)
9X-RAY DIFFRACTION9(chain P and resid 1112:1122)

+
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