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- PDB-4jan: crystal structure of broadly neutralizing antibody CH103 in compl... -

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Basic information

Entry
Database: PDB / ID: 4jan
Titlecrystal structure of broadly neutralizing antibody CH103 in complex with HIV-1 gp120
Components
  • (ANTIGEN BINDING FRAGMENT OF ...) x 2
  • ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
Keywordsviral protein/immune system / HIV-1 / gp120 / GLYCOPROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / Antibody / immunoglobulin / NEUTRALIZATION / VACCINE
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane
Similarity search - Function
Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsZhou, T. / Moquin, S. / Zheng, A. / Srivatsan, S. / Kwong, P.D.
CitationJournal: Nature / Year: 2013
Title: Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus.
Authors: Liao, H.X. / Lynch, R. / Zhou, T. / Gao, F. / Alam, S.M. / Boyd, S.D. / Fire, A.Z. / Roskin, K.M. / Schramm, C.A. / Zhang, Z. / Zhu, J. / Shapiro, L. / Mullikin, J.C. / Gnanakaran, S. / ...Authors: Liao, H.X. / Lynch, R. / Zhou, T. / Gao, F. / Alam, S.M. / Boyd, S.D. / Fire, A.Z. / Roskin, K.M. / Schramm, C.A. / Zhang, Z. / Zhu, J. / Shapiro, L. / Mullikin, J.C. / Gnanakaran, S. / Hraber, P. / Wiehe, K. / Kelsoe, G. / Yang, G. / Xia, S.M. / Montefiori, D.C. / Parks, R. / Lloyd, K.E. / Scearce, R.M. / Soderberg, K.A. / Cohen, M. / Kamanga, G. / Louder, M.K. / Tran, L.M. / Chen, Y. / Cai, F. / Chen, S. / Moquin, S. / Du, X. / Joyce, M.G. / Srivatsan, S. / Zhang, B. / Zheng, A. / Shaw, G.M. / Hahn, B.H. / Kepler, T.B. / Korber, B.T. / Kwong, P.D. / Mascola, J.R. / Haynes, B.F.
History
DepositionFeb 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2May 1, 2013Group: Database references
Revision 1.3May 29, 2013Group: Database references
Revision 1.4Jul 16, 2014Group: Other
Revision 1.5Jan 9, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.8Nov 27, 2024Group: Data collection / Structure summary
Category: diffrn_detector / pdbx_entry_details / pdbx_modification_feature
Item: _diffrn_detector.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
H: ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN of CH103
L: ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN of CH103
I: ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
A: ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN of CH103
B: ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN of CH103
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,85020
Polymers171,4086
Non-polymers2,44214
Water39622
1
G: ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
H: ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN of CH103
L: ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN of CH103
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,94811
Polymers85,7043
Non-polymers1,2448
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
A: ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN of CH103
B: ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN of CH103
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9029
Polymers85,7043
Non-polymers1,1986
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.943, 208.651, 69.422
Angle α, β, γ (deg.)90.00, 107.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules HALB

#2: Antibody ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN of CH103


Mass: 23896.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: CMVR-based / Cell line (production host): 293F / Production host: HOMO SAPIENS (human)
#3: Antibody ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN of CH103


Mass: 22533.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: CMVR-based / Cell line (production host): 293F / Production host: HOMO SAPIENS (human)

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Protein / Sugars , 2 types, 12 molecules GI

#1: Protein ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C


Mass: 39273.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Strain: ZM176.55 / Plasmid: CMVR-based / Cell line (production host): 293F / Production host: HOMO SAPIENS (human) / References: UniProt: R4GRV3*PLUS
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 26 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.98 Å3/Da / Density % sol: 37.73 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 200 mM sodium formate, 20% PEG 3350 and 100 mM Bistrispropane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Jul 22, 2012 / Details: APS 22ID
RadiationMonochromator: APS 22ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 20488 / % possible obs: 89.4 % / Observed criterion σ(I): 1.4 / Redundancy: 3.4 % / Biso Wilson estimate: 61.3 Å2 / Rsym value: 0.134 / Net I/σ(I): 10
Reflection shellResolution: 3.21→3.25 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.31 / % possible all: 59

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGB

3ngb


Resolution: 3.15→46.75 Å / SU ML: 0.4 / σ(F): 1.37 / Phase error: 28.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 1042 5.1 %
Rwork0.196 --
obs0.199 20444 89.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8843 0 154 22 9019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029211
X-RAY DIFFRACTIONf_angle_d0.6112519
X-RAY DIFFRACTIONf_dihedral_angle_d11.3453317
X-RAY DIFFRACTIONf_chiral_restr0.0381464
X-RAY DIFFRACTIONf_plane_restr0.0031576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1493-3.31530.316790.26091539X-RAY DIFFRACTION49
3.3153-3.5230.31411100.25312411X-RAY DIFFRACTION78
3.523-3.79490.29721800.23933017X-RAY DIFFRACTION97
3.7949-4.17650.30921730.20363075X-RAY DIFFRACTION100
4.1765-4.78040.21151590.16763119X-RAY DIFFRACTION100
4.7804-6.02070.23251740.17713120X-RAY DIFFRACTION100
6.0207-46.75650.23091670.17653121X-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)
14.49620.37351.00914.5709-0.55892.83660.3015-0.1621-0.30221.002-0.3565-0.32081.18790.33180.05931.87530.34280.03840.83180.13150.660626.5414-39.960937.2219
25.7981-0.49710.76166.23951.23125.08050.9032-0.16330.76220.6914-0.61340.599-1.7356-0.8241-0.23221.44260.11120.4660.8238-0.01850.845810.980651.366-3.8035
35.7930.06361.11634.35610.83515.7281-0.04280.5344-0.3718-0.6291-0.4013-0.02480.7741-0.02620.40981.00920.25190.08980.57360.03430.428319.4631-21.090911.4302
42.79370.8886-1.53455.7009-2.20464.1080.0890.14530.02730.1528-0.0222-0.0174-0.1782-0.2829-0.0670.2561-0.0348-0.06720.5702-0.00690.246516.092119.12975.4647
51.7395-0.80221.11196.1813-0.30181.361-0.15610.3295-0.0225-0.1422-0.0816-1.18360.6421.23470.20410.59480.32780.13570.93550.12830.733636.8762-11.085721.662
64.434-2.2493-2.33174.67550.76254.0408-0.0051-0.1278-0.0180.13920.0271-0.21140.0030.1252-0.05390.29710.0242-0.11030.65430.03720.315120.004713.737120.2043
76.1106-2.3504-1.01847.08010.86434.80320.18770.58530.436-0.0415-0.1228-0.4538-0.82920.4007-0.03970.4146-0.10250.04240.56930.06040.314831.237431.7877-20.9984
83.83852.11150.4538.34911.6856.3883-0.1952-0.1009-0.05820.024-0.09710.11220.70520.4740.32270.37320.10320.03930.6530.01180.304636.5438-8.2271-24.5938
93.58772.36563.25726.62731.48224.41380.28520.57130.1384-0.0462-0.1650.4693-0.2082-0.9735-0.0620.26930.11420.00910.88740.04980.351110.978722.6599-22.5778
108.1473-1.6518-0.55145.3605-0.97414.05930.1275-0.0866-0.09250.3073-0.35530.26530.76940.62270.21610.43650.13740.04110.524-0.02020.316224.8781-2.7199-14.323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain G and resid 252:475
2X-RAY DIFFRACTION2chain I and resid 252:475
3X-RAY DIFFRACTION3chain H and resid 1:113
4X-RAY DIFFRACTION4chain H and resid 114:223
5X-RAY DIFFRACTION5chain L and resid 1:108
6X-RAY DIFFRACTION6chain L and resid 109:215
7X-RAY DIFFRACTION7chain A and resid 1:113
8X-RAY DIFFRACTION8chain A and resid 114:223
9X-RAY DIFFRACTION9chain B and resid 1:108
10X-RAY DIFFRACTION10chain B and resid 109:215

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