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- PDB-7kx4: Anti-CCHFV ADI-36121 Fab -

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Basic information

Entry
Database: PDB / ID: 7kx4
TitleAnti-CCHFV ADI-36121 Fab
Components
  • ADI-36121 Fab heavy chain
  • ADI-36121 Fab light chain
KeywordsIMMUNE SYSTEM / antibody / Fab
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsMishra, A.K. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI142777 United States
CitationJournal: Science / Year: 2022
Title: Structural basis of synergistic neutralization of Crimean-Congo hemorrhagic fever virus by human antibodies.
Authors: Mishra, A.K. / Hellert, J. / Freitas, N. / Guardado-Calvo, P. / Haouz, A. / Fels, J.M. / Maurer, D.P. / Abelson, D.M. / Bornholdt, Z.A. / Walker, L.M. / Chandran, K. / Cosset, F.L. / McLellan, J.S. / Rey, F.A.
History
DepositionDec 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADI-36121 Fab light chain
B: ADI-36121 Fab heavy chain
C: ADI-36121 Fab light chain
D: ADI-36121 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)96,1614
Polymers96,1614
Non-polymers00
Water5,729318
1
A: ADI-36121 Fab light chain
D: ADI-36121 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)48,0812
Polymers48,0812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-21 kcal/mol
Surface area19240 Å2
MethodPISA
2
B: ADI-36121 Fab heavy chain
C: ADI-36121 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,0812
Polymers48,0812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-22 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.190, 76.640, 208.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 99 or resid 101...
21(chain C and (resid 1 through 99 or resid 101...
12(chain B and (resid 1 through 18 or resid 20...
22(chain D and (resid 1 through 18 or resid 20...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPGLYGLY(chain A and (resid 1 through 99 or resid 101...AA1 - 991 - 99
121GLYGLYVALVAL(chain A and (resid 1 through 99 or resid 101...AA101 - 104101 - 104
131ILEILEHISHIS(chain A and (resid 1 through 99 or resid 101...AA106 - 189106 - 189
141VALVALGLUGLU(chain A and (resid 1 through 99 or resid 101...AA191 - 213191 - 213
211ASPASPGLYGLY(chain C and (resid 1 through 99 or resid 101...CC1 - 991 - 99
221GLYGLYVALVAL(chain C and (resid 1 through 99 or resid 101...CC101 - 104101 - 104
231ILEILEHISHIS(chain C and (resid 1 through 99 or resid 101...CC106 - 189106 - 189
241VALVALGLUGLU(chain C and (resid 1 through 99 or resid 101...CC191 - 213191 - 213
112GLUGLULEULEU(chain B and (resid 1 through 18 or resid 20...BB1 - 181 - 18
122LEULEUGLYGLY(chain B and (resid 1 through 18 or resid 20...BB20 - 4220 - 42
132GLYGLYTHRTHR(chain B and (resid 1 through 18 or resid 20...BB44 - 5744 - 57
142TYRTYRHISHIS(chain B and (resid 1 through 18 or resid 20...BB59 - 20059 - 205
152PROPROTHRTHR(chain B and (resid 1 through 18 or resid 20...BB202 - 205207 - 210
162VALVALLYSLYS(chain B and (resid 1 through 18 or resid 20...BB207 - 209212 - 214
172VALVALPROPRO(chain B and (resid 1 through 18 or resid 20...BB211 - 213216 - 218
182SERSERSERSER(chain B and (resid 1 through 18 or resid 20...BB215220
212GLUGLULEULEU(chain D and (resid 1 through 18 or resid 20...DD1 - 181 - 18
222LEULEUGLYGLY(chain D and (resid 1 through 18 or resid 20...DD20 - 4220 - 42
232GLYGLYTHRTHR(chain D and (resid 1 through 18 or resid 20...DD44 - 5744 - 57
242GLUGLUSERSER(chain D and (resid 1 through 18 or resid 20...DD1 - 2151 - 220
252GLUGLUSERSER(chain D and (resid 1 through 18 or resid 20...DD1 - 2151 - 220
262VALVALLYSLYS(chain D and (resid 1 through 18 or resid 20...DD207 - 209212 - 214
272SERSERSERSER(chain D and (resid 1 through 18 or resid 20...DD215220

NCS ensembles :
ID
1
2

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Components

#1: Antibody ADI-36121 Fab light chain


Mass: 23416.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody ADI-36121 Fab heavy chain


Mass: 24663.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MgCl2, 0.1 M CaCl2, 0.1 M KNa Tartrate, 25% PEG 4000, 4% isopropanol, 0.1 M Bis-Tris-HCl pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→51.5 Å / Num. obs: 29766 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 29.99 Å2 / CC1/2: 0.987 / Net I/σ(I): 8.1
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 29695 / CC1/2: 0.736

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.19_4080refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I19, 1HEZ

5i19

1hez


Resolution: 2.6→51.49 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 1476 4.97 %
Rwork0.1979 28220 -
obs0.2 29696 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.61 Å2 / Biso mean: 36.5091 Å2 / Biso min: 16.18 Å2
Refinement stepCycle: final / Resolution: 2.6→51.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6524 0 0 318 6842
Biso mean---30.37 -
Num. residues----856
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1250X-RAY DIFFRACTION1.385TORSIONAL
12C1250X-RAY DIFFRACTION1.385TORSIONAL
21B1204X-RAY DIFFRACTION1.385TORSIONAL
22D1204X-RAY DIFFRACTION1.385TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.680.32211480.264325112659
2.68-2.780.32551230.26225442667
2.78-2.890.31471060.256125302636
2.89-3.020.28661280.24125392667
3.02-3.180.26271180.215925522670
3.18-3.380.24061230.20625252648
3.38-3.640.24241680.19625492717
3.64-40.23141340.18425502684
4-4.580.20051370.15525792716
4.58-5.770.18551450.153225982743
5.77-51.490.21611460.195327432889
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)
11.37480.4429-1.75251.77030.26255.5159-0.7962-0.4166-0.01510.94480.4884-0.48560.60750.05130.09270.85420.4487-0.07340.7636-0.07080.3125-15.630224.9243-4.8754
20.01870.8553-0.0171.8019-0.49372.42460.02490.0771-0.003-0.113-0.0349-0.27850.65030.05760.01820.17250.0130.04750.19-0.04430.2551.33913.8501-55.0874
32.27350.3461-1.19471.4545-0.20424.30530.1354-0.11480.15190.14110.0603-0.2879-0.15410.4099-0.14930.1295-0.0059-0.03690.1051-0.01450.26935.558322.4947-51.7978
41.4628-0.349-1.07181.5811-1.48922.9422-0.0392-0.35670.0680.07340.0369-0.2467-0.71170.79990.04940.1846-0.0765-0.10060.2168-0.00150.24497.864215.7402-46.967
52.48960.81271.08273.6679-1.46966.5062-0.17160.12950.2028-0.40160.39120.15270.0332-0.5955-0.15220.1176-0.00330.01920.12680.02260.2235-5.627623.3641-56.0683
60.42080.3107-0.61843.69870.40242.25030.0183-0.3653-0.2161.966-0.8107-0.66821.0686-0.3109-0.2947-0.58610.3065-0.1480.05470.08520.31721.6385.5255-36.8688
74.81340.0660.38062.98370.01773.9554-0.0551-0.2962-0.38770.52440.04430.55030.0598-0.39050.01750.31090.02970.10340.1876-0.00060.24-19.1151-2.6661-29.558
85.03490.08480.40711.4773-0.45530.6703-0.47861.66580.8388-0.12230.27930.5035-0.18650.13060.02850.1760.0655-0.02320.2124-0.00670.3148-17.27712.3869-39.689
95.6553-0.32540.5823.0934-0.16644.56440.1257-0.2412-0.12130.2442-0.10580.41510.154-0.3301-0.1050.26570.04420.07910.1567-0.00560.2621-17.2578-0.0897-34.3091
109.0614-0.5822-2.83511.32862.03573.6657-0.6747-0.0837-1.03560.708-0.1398-0.47510.9333-0.39140.52150.4190.05260.06080.2582-0.04850.4361-17.5548-9.382-34.8962
114.28970.6425-2.6342.1325-1.29743.4582-0.1609-0.05450.0069-0.03610.0766-0.02490.0174-0.08560.02260.13350.0344-0.03640.1038-0.05660.1532-15.77230.8054-46.0961
123.9655-1.67441.42314.5516-1.4872.5679-0.05-0.39510.15510.62290.06110.048-0.0320.2245-0.07750.40660.06920.12770.3268-0.05460.2674-21.48475.2255-20.5299
133.8962-2.0728-0.60672.8407-1.53274.6024-0.1472-0.64170.08740.39270.24640.3936-0.1110.0468-0.15090.25120.0440.06020.34040.04740.2087-46.067949.4122-20.7832
141.9267-0.4506-0.59753.6657-0.10933.9469-0.43120.1298-0.51071.10930.5619-0.6085-0.3635-0.0407-0.030.78410.3512-0.12560.7052-0.17570.3595-20.698534.82851.8737
154.6194-0.4023-3.80893.1073-0.87134.1362-0.1281-0.38230.40980.720.4182-0.3833-0.7089-0.4707-0.26730.88610.389-0.09080.7568-0.10570.362-23.427640.6452-0.6204
164.9984-1.7797-1.07893.30730.08882.2533-0.09040.08180.1744-0.16420.122-0.1435-0.0327-0.1451-0.02730.20680.02010.04950.11470.03120.1123-29.608845.4486-34.741
170.6968-1.2262-0.01572.2947-0.60195.5656-0.5799-0.3677-0.18680.33410.4036-0.14051.50480.03170.10230.63270.2883-0.10260.5714-0.06690.3599-17.954526.8623-8.1161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 164 through 213 )C164 - 213
2X-RAY DIFFRACTION2chain 'D' and (resid 1 through 33 )D1 - 33
3X-RAY DIFFRACTION3chain 'D' and (resid 34 through 75 )D34 - 75
4X-RAY DIFFRACTION4chain 'D' and (resid 76 through 87 )D76 - 87
5X-RAY DIFFRACTION5chain 'D' and (resid 88 through 106 )D88 - 106
6X-RAY DIFFRACTION6chain 'D' and (resid 107 through 119 )D107 - 119
7X-RAY DIFFRACTION7chain 'D' and (resid 120 through 145 )D120 - 145
8X-RAY DIFFRACTION8chain 'D' and (resid 146 through 165 )D146 - 165
9X-RAY DIFFRACTION9chain 'D' and (resid 166 through 203 )D166 - 203
10X-RAY DIFFRACTION10chain 'D' and (resid 204 through 215 )D204 - 215
11X-RAY DIFFRACTION11chain 'A' and (resid 1 through 113 )A1 - 113
12X-RAY DIFFRACTION12chain 'A' and (resid 114 through 213 )A114 - 213
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 119 )B1 - 119
14X-RAY DIFFRACTION14chain 'B' and (resid 120 through 145 )B120 - 145
15X-RAY DIFFRACTION15chain 'B' and (resid 146 through 215 )B146 - 215
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 101 )C1 - 101
17X-RAY DIFFRACTION17chain 'C' and (resid 102 through 163 )C102 - 163

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