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- PDB-5ea0: Structure of the antibody 7968 with human complement factor H-der... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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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)

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