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- PDB-8vvk: CCHFV GP38 bound to ADI-46143 Fab -

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Basic information

Entry
Database: PDB / ID: 8vvk
TitleCCHFV GP38 bound to ADI-46143 Fab
Components
  • (ADI-46143 Fab ...) x 2
  • GP38
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / CCHFV / GP38 / Antibody / Immunology / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell Golgi membrane / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
: / : / : / : / Nairovirus, structural glycoprotein Gn / Nairovirus, mucin-like domain / Nairovirus NSm / Nairovirus M polyprotein-like / Nairovirus GP38 / : ...: / : / : / : / Nairovirus, structural glycoprotein Gn / Nairovirus, mucin-like domain / Nairovirus NSm / Nairovirus M polyprotein-like / Nairovirus GP38 / : / Hantavirus glycoprotein Gc, C-terminal / Hantavirus glycoprotein Gc / Hantavirus glycoprotein Gc, N-terminal
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsHjorth, C.K. / McLellan, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI152246 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI142777 United States
CitationJournal: To Be Published
Title: Crimean-Congo Hemorrhagic Fever Survivors Elicit Protective Non-Neutralizing Antibodies that Target 11 Overlapping Regions on Viral Glycoprotein GP38
Authors: Shin, O.S. / Monticelli, S.R. / Hjorth, C.K. / Hornet, V. / Doyle, M. / Abelson, D. / Kuehne, A.I. / Wang, A. / Bakken, R.R. / Mishra, A.K. / Middlecamp, M. / Champney, E. / Stuart, L. / ...Authors: Shin, O.S. / Monticelli, S.R. / Hjorth, C.K. / Hornet, V. / Doyle, M. / Abelson, D. / Kuehne, A.I. / Wang, A. / Bakken, R.R. / Mishra, A.K. / Middlecamp, M. / Champney, E. / Stuart, L. / Maurer, D.P. / Li, J. / Berrigan, J.L. / Balinandi, S. / Lutwama, J.J. / Lobel, L. / Zeitlin, L. / Walker, L.M. / Dye, J.M. / Chandran, K. / Herbert, A.S. / Pauli, N.T. / McLellan, J.S.
History
DepositionJan 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GP38
B: GP38
C: ADI-46143 Fab Light Chain
D: ADI-46143 Fab Heavy Chain
H: ADI-46143 Fab Heavy Chain
L: ADI-46143 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,74610
Polymers152,8866
Non-polymers1,8604
Water4,270237
1
A: GP38
H: ADI-46143 Fab Heavy Chain
L: ADI-46143 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2925
Polymers76,4433
Non-polymers8492
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GP38
C: ADI-46143 Fab Light Chain
D: ADI-46143 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4545
Polymers76,4433
Non-polymers1,0112
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.647, 149.647, 315.727
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

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Antibody , 2 types, 4 molecules CLDH

#2: Antibody ADI-46143 Fab Light Chain


Mass: 22471.824 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: Antibody ADI-46143 Fab Heavy Chain


Mass: 23729.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 239 molecules AB

#1: Protein GP38


Mass: 30241.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus / Strain: IbAr10200 / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: Q8JSZ3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 4 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Details

Has ligand of interestN

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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: 3.34 Å3/Da / Density % sol: 63.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium Citrate pH 7.5, 9.3% (w/v) PEG 3350, 12.6% (v/v) 2-Propanol

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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: Jul 15, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.61→59.95 Å / Num. obs: 64162 / % possible obs: 99.93 % / Redundancy: 2 % / Biso Wilson estimate: 49.12 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02675 / Rpim(I) all: 0.02675 / Rrim(I) all: 0.03784 / Net I/σ(I): 15.64
Reflection shellResolution: 2.61→2.703 Å / Redundancy: 2 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 2.81 / Num. unique obs: 6283 / CC1/2: 0.814 / CC star: 0.947 / Rpim(I) all: 0.262 / Rrim(I) all: 0.3706 / % possible all: 99.86

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→59.95 Å / SU ML: 0.2805 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3504
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2174 3178 4.94 %
Rwork0.1771 61163 -
obs0.1791 64162 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.33 Å2
Refinement stepCycle: LAST / Resolution: 2.61→59.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10294 0 123 237 10654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005410650
X-RAY DIFFRACTIONf_angle_d0.74114468
X-RAY DIFFRACTIONf_chiral_restr0.04941669
X-RAY DIFFRACTIONf_plane_restr0.00561823
X-RAY DIFFRACTIONf_dihedral_angle_d5.60861496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.650.32451280.25252611X-RAY DIFFRACTION100
2.65-2.690.31991450.24492595X-RAY DIFFRACTION99.85
2.69-2.730.31181540.23342587X-RAY DIFFRACTION99.82
2.73-2.780.28861350.23282621X-RAY DIFFRACTION99.86
2.78-2.830.29031380.22542598X-RAY DIFFRACTION99.96
2.83-2.880.30581150.21252644X-RAY DIFFRACTION99.93
2.88-2.940.28041490.22242593X-RAY DIFFRACTION99.96
2.94-3.010.30541290.21942635X-RAY DIFFRACTION99.89
3.01-3.080.27621250.21542621X-RAY DIFFRACTION100
3.08-3.150.25381290.20672632X-RAY DIFFRACTION99.96
3.15-3.240.27521350.19892644X-RAY DIFFRACTION100
3.24-3.330.21771250.20012646X-RAY DIFFRACTION100
3.33-3.440.26021530.19472609X-RAY DIFFRACTION100
3.44-3.560.22271480.18622667X-RAY DIFFRACTION100
3.56-3.710.24051330.17882632X-RAY DIFFRACTION100
3.71-3.880.18511270.17392653X-RAY DIFFRACTION99.93
3.88-4.080.19611320.15592681X-RAY DIFFRACTION100
4.08-4.340.19311540.14332648X-RAY DIFFRACTION100
4.34-4.670.15011270.12642713X-RAY DIFFRACTION99.96
4.67-5.140.15151600.13472680X-RAY DIFFRACTION100
5.14-5.880.19791360.1482733X-RAY DIFFRACTION100
5.88-7.410.1941620.18452755X-RAY DIFFRACTION100
7.41-59.950.19511390.17692965X-RAY DIFFRACTION99.68
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)
14.09232722664-1.317688567941.541870023395.3939019466-2.769639727973.63685725039-0.0305496103961-0.2631303967570.2120335186770.2420050897860.1643298016060.526848344349-0.186045165252-0.526260496325-0.130550960070.270502367278-0.02441480911170.002301104537840.5283970865260.02183067235010.375824398413-130.91679532.702923805912.716117711
24.170596669-0.297890814855-0.9115472746532.943055564031.039804096034.99636138180.06400080467390.02769641051440.2792219932880.0339103286993-0.09070815663280.0272673907096-0.2818482804330.002879295091070.02866529630420.276814105059-0.00376747652107-0.001668306873530.2859969193320.01410322269780.188045486047-94.23570405638.570926305214.6485896363
33.305810091141.080125606630.2657744549925.902762495851.045495791333.28517645338-0.270801559461-0.2839215414960.2756924395150.4131081096870.3766054791520.2787462293590.0262025423261-0.549046681654-0.1019586219620.356362161540.1381493243230.02287476684060.6351859358050.01004349277350.380331233597-130.80481853336.631601357928.5197618764
48.19269958421-2.03334498327-0.8785006298084.443377544460.2490334616813.912681858320.3753984118120.2992696536430.0115775908125-0.473872347654-0.35557207780.221619226289-0.6230730582250.08937185496140.002401118220.633216899654-0.0293289388183-0.04626324560050.312583688111-0.02276542715790.364362310694-23.338007085296.701846359134.8346176984
55.62500996669-1.735923786311.823572953551.37276993335-0.3416229512942.542482168160.2173929294680.9792221329360.0819616492111-0.128630825497-0.163644895269-0.3638099756790.03270225225880.702480386451-0.052201874370.4299371452260.01665676780080.04268361415540.61259191743-0.03707276380540.399574787162-56.783028625121.6255647140.642807034058
62.769693791591.354726982731.472943391984.243118669332.212841149874.206201452980.339182198492-0.0952874950937-0.4857236885810.27255351651-0.148472645555-0.1211443805060.70788655733-0.300443135562-0.1819103522580.472829966032-0.0643835434796-0.07486246387580.3813176970150.03868232523520.416744532993-43.327118195218.299230494735.4383123534
73.93210178321-0.7605664479350.4687280474565.82969069436-0.567892998812.4709343399-0.0445990708933-0.06384698841170.2387408231140.1458630949550.02769314568430.582658634844-0.118803160949-0.2129627943250.001815707664990.250545182393-0.02836988267390.006280631741740.3312129465810.04233028002740.313795844515-41.309740089662.418720080139.3406391961
82.778191200991.2466962041-0.4619731921253.072043552-1.604068682422.459330371630.04678814541570.152621797192-0.09225202945270.008478838561060.0549131056704-0.1104241011610.05916036858490.0654511596521-0.05201582092890.306407403599-0.0224426099846-0.03811110906230.311365461646-0.07328125817090.276700779767-20.10059388956.936540640442.2015411936
93.07770208278-2.97653305294-3.132244622586.504823909965.034556058447.453075125630.0478359021046-0.1313374057840.20516197330.1137537258930.1186371550360.0847810960278-0.3143529804530.209498069452-0.1625940799290.30810174183-0.119129454756-0.002143616503130.3533257280390.02786120819650.306867616051-17.034506492388.400254758747.1204193866
105.280737799361.80979604154-1.395022841872.52500839996-0.6989745382863.04519005163-7.10231444728E-50.288118533802-0.518754125372-0.162497946097-0.0350962286408-0.05518111851750.322686420925-0.07137940428210.04828965902890.3322307114180.0433904585806-0.06790485520710.285152872671-0.05569642598940.309728699456-101.95494543320.29780002245.08578546832
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'H' and resid 114 through 214)HN114 - 214124 - 224
22(chain 'L' and resid 1 through 106A)LO1 - 1061 - 108
33(chain 'L' and resid 107 through 208)LO107 - 208109 - 210
44(chain 'C' and resid 109 through 208)CL109 - 208111 - 210
55(chain 'A' and resid 253 through 512)AA253 - 5121 - 240
66(chain 'B' and resid 253 through 515)BF253 - 5151 - 240
77(chain 'C' and resid 1 through 108)CL1 - 1081 - 110
88(chain 'D' and resid 1 through 113)DM1 - 1131 - 123
99(chain 'D' and resid 114 through 213)DM114 - 213124 - 223
1010(chain 'H' and resid 1 through 113)HN1 - 1131 - 123

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