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- PDB-6vmj: Crystal structure of human Complement Factor D with anti-Factor D... -

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Basic information

Entry
Database: PDB / ID: 6vmj
TitleCrystal structure of human Complement Factor D with anti-Factor D Fab 20D12
Components
  • Complement factor D
  • Fab20D12 Light Chain
  • Fab20D12 heavy chain
KeywordsHYDROLASE/IMMUNE SYSTEM / CFD / Factor D / Fab / HYDROLASE / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


complement factor D / Alternative complement activation / complement activation / complement activation, alternative pathway / serine-type peptidase activity / platelet alpha granule lumen / protein maturation / response to bacterium / Platelet degranulation / secretory granule lumen ...complement factor D / Alternative complement activation / complement activation / complement activation, alternative pathway / serine-type peptidase activity / platelet alpha granule lumen / protein maturation / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Complement factor D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsWu, P. / Harris, S.F. / Eigenbrot, C.
CitationJournal: To Be Published
Title: Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12
Authors: Dion, M. / Wu, P. / Morando, A. / Bullen, G. / Shatz, W. / Harris, S.F. / Eigenbrot, C. / Loyet, K.M. / Yadav, D. / Tassew, N. / Booler, H. / Scheer, J. / Kelley, R.F. / Tesar, D.B.
History
DepositionJan 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab20D12 Light Chain
B: Fab20D12 heavy chain
E: Fab20D12 Light Chain
F: Fab20D12 heavy chain
I: Fab20D12 Light Chain
J: Fab20D12 heavy chain
L: Fab20D12 Light Chain
M: Fab20D12 heavy chain
W: Complement factor D
X: Complement factor D
Y: Complement factor D
Z: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,02518
Polymers285,87212
Non-polymers1,1536
Water2,720151
1
A: Fab20D12 Light Chain
B: Fab20D12 heavy chain
Z: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6604
Polymers71,4683
Non-polymers1921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Fab20D12 Light Chain
F: Fab20D12 heavy chain
Y: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6604
Polymers71,4683
Non-polymers1921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Fab20D12 Light Chain
J: Fab20D12 heavy chain
X: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8525
Polymers71,4683
Non-polymers3842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
L: Fab20D12 Light Chain
M: Fab20D12 heavy chain
W: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8525
Polymers71,4683
Non-polymers3842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.843, 180.843, 304.189
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody
Fab20D12 Light Chain


Mass: 23360.787 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody
Fab20D12 heavy chain


Mass: 23668.393 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein
Complement factor D / Adipsin / C3 convertase activator / Properdin factor D


Mass: 24438.807 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFD, DF, PFD / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00746, complement factor D
#4: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.35 Å3/Da / Density % sol: 71.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M sodium cacodylate pH 6.5, 1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 106295 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 55.3 Å2 / Rmerge(I) obs: 0.135 / Χ2: 1.018 / Net I/σ(I): 7 / Num. measured all: 767163
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.95-3.066.50.633104621.063199.8
3.06-3.186.60.464104651.1199.8
3.18-3.326.80.359104791.104199.9
3.32-3.56.90.243105171.076199.9
3.5-3.7270.199105481.082199.9
3.72-47.20.161105791.0781100
4-4.417.50.117106090.9711100
4.41-5.047.90.088106500.8441100
5.04-6.357.80.076107720.9471100
6.35-507.90.042112140.979199.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
BUSTER2.11.5refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D9R

4d9r


Resolution: 2.95→47.24 Å / Cor.coef. Fo:Fc: 0.9177 / Cor.coef. Fo:Fc free: 0.8686 / SU R Cruickshank DPI: 0.563 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.54 / SU Rfree Blow DPI: 0.332 / SU Rfree Cruickshank DPI: 0.34
RfactorNum. reflection% reflectionSelection details
Rfree0.2652 1050 0.99 %RANDOM
Rwork0.2175 ---
obs0.218 105651 99.36 %-
Displacement parametersBiso max: 172.25 Å2 / Biso mean: 53.17 Å2 / Biso min: 8.89 Å2
Baniso -1Baniso -2Baniso -3
1--6.6529 Å20 Å20 Å2
2---6.6529 Å20 Å2
3---13.3058 Å2
Refine analyzeLuzzati coordinate error obs: 0.498 Å
Refinement stepCycle: final / Resolution: 2.95→47.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19699 0 78 151 19928
Biso mean--92.08 29.78 -
Num. residues----2610
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6737SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes440HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2984HARMONIC5
X-RAY DIFFRACTIONt_it20239HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2633SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact22140SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d20239HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg27565HARMONIC21.22
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion19.53
LS refinement shellResolution: 2.95→3.03 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3291 66 0.86 %
Rwork0.2905 7568 -
all0.2909 7634 -
obs--99.36 %
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)
11.48690.3601-0.62762.4449-0.47490.85530.0448-0.3542-0.20090.0559-0.2783-0.31490.11310.45060.2335-0.12470.08760.03030.22540.1391-0.19063.7342-75.793128.9165
22.24340.5119-0.97571.4039-0.62540.892-0.33610.0589-0.3522-0.27360.1284-0.17790.45040.12330.20760.27380.03270.152-0.22210.0124-0.2114-15.034-97.5391-14.5099
31.9856-0.60990.35520.66650.18121.80390.0308-0.10320.10120.0166-0.0780.0318-0.00290.16970.04730.0240.00870.0512-0.01680.0318-0.0879-9.9092-51.6451-1.6514
40.7830.0158-0.11121.37380.21860.7245-0.0885-0.02280.0582-0.157-0.00560.10180.1894-0.04740.09410.1347-0.03680.0328-0.0880.0292-0.0616-40.5693-89.297216.8246
51.0246-0.0516-0.68591.3434-1.12.4837-0.0897-0.2403-0.1933-0.317-0.2401-0.37520.49640.29180.32970.08050.1520.152-0.17110.152-0.0549-7.9964-112.0824.4298
61.1549-0.318-0.64790.6667-0.77332.7877-0.1536-0.0908-0.2598-0.2221-0.1658-0.06190.30260.54420.3195-0.07640.1520.1520.07060.152-0.125118.4742-79.2867-10.2605
70.5862-0.1582-0.62220.0051-0.55281.65060.03130.08170.015-0.10930.0950.1610.2118-0.3007-0.12640.1224-0.0315-0.0337-0.05630.0183-0.0629-40.5779-66.9607-18.8581
80.72710.1872-0.4870.9799-0.4931.50990.05090.00210.03270.0184-0.01830.082-0.10270.0737-0.03260.01430.01630.02210.007-0.0247-0.0425-31.1334-56.474834.4772
900.24390.77325.83410.67912.76530.05660.0093-0.3826-0.36160.431-0.01250.54420.0774-0.48760.3040.1170.152-0.3040.152-0.304-13.7964-145.0614.7563
104.92771.84140.376200.01870.83720.1888-0.27250.40770.07990.1666-0.0406-0.0160.5442-0.3554-0.3040.02310.1520.2980.152-0.006950.1377-67.9221-1.6486
112.98921.28090.45612.2258-1.02652.58730.20010.0902-0.217-0.09410.1440.31460.5442-0.383-0.3441-0.0131-0.139-0.0753-0.12180.031-0.0848-72.1256-78.2234-28.1658
121.3512-0.3145-0.23472.14020.67852.2047-0.04590.03070.10920.04830.144-0.1115-0.13080.0933-0.0981-0.01270.0252-0.0001-0.074-0.0441-0.0683-32.8107-22.395438.9439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{Z|16 - Z|243}Z16 - 243
2X-RAY DIFFRACTION2{Y|16 - Y|243}Y16 - 243
3X-RAY DIFFRACTION3{X|16 - X|243}X16 - 243
4X-RAY DIFFRACTION4{W|16 - W|243}W16 - 243
5X-RAY DIFFRACTION5{A|1 - A|107 B|1 - B|114}A1 - 107
6X-RAY DIFFRACTION5{A|1 - A|107 B|1 - B|114}B1 - 114
7X-RAY DIFFRACTION6{E|1 - E|107 F|1 - F|114}E1 - 107
8X-RAY DIFFRACTION6{E|1 - E|107 F|1 - F|114}F1 - 114
9X-RAY DIFFRACTION7{I|1 - I|107 J|1 - J|114}I1 - 107
10X-RAY DIFFRACTION7{I|1 - I|107 J|1 - J|114}J1 - 114
11X-RAY DIFFRACTION8{L|1 - L|107 M|1 - M|114}L1 - 107
12X-RAY DIFFRACTION8{L|1 - L|107 M|1 - M|114}M1 - 114
13X-RAY DIFFRACTION9{A|108 - A|213 B|115 - B|213}A108 - 213
14X-RAY DIFFRACTION9{A|108 - A|213 B|115 - B|213}B115 - 213
15X-RAY DIFFRACTION10{E|108 - E|213 F|115 - F|213}E108 - 213
16X-RAY DIFFRACTION10{E|108 - E|213 F|115 - F|213}F115 - 213
17X-RAY DIFFRACTION11{I|108 - I|213 J|115 - J|213}I108 - 213
18X-RAY DIFFRACTION11{I|108 - I|213 J|115 - J|213}J115 - 213
19X-RAY DIFFRACTION12{L|108 - L|213 M|115 - M|215}L108 - 213
20X-RAY DIFFRACTION12{L|108 - L|213 M|115 - M|215}M115 - 215

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