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- PDB-4lsq: Crystal structure of broadly and potently neutralizing antibody V... -

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Basic information

Entry
Database: PDB / ID: 4lsq
TitleCrystal structure of broadly and potently neutralizing antibody VRC-CH31 in complex with HIV-1 clade A/E gp120 93TH057 with LOOP D and Loop V5 from clade A strain 3415_v1_c1
Components
  • ENVELOPE GLYCOPROTEIN GP120 WITH LOOP D AND V5 FROM STRAIN 3415_V1_C1
  • HEAVY CHAIN OF ANTIBODY VRC-CH31
  • LIGHT CHAIN OF ANTIBODY VRC-CH31 WITH N70D MUTATION
Keywordsviral protein/immune system / Neutralizing antibody VRC-CH31 / viral protein-immune system complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins ...HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / : / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsZhou, T. / Moquin, S. / Kwong, P.D.
CitationJournal: Immunity / Year: 2013
Title: Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway for HIV-1 Neutralization by VRC01-Class Antibodies.
Authors: Zhou, T. / Zhu, J. / Wu, X. / Moquin, S. / Zhang, B. / Acharya, P. / Georgiev, I.S. / Altae-Tran, H.R. / Chuang, G.Y. / Joyce, M.G. / Do Kwon, Y. / Longo, N.S. / Louder, M.K. / Luongo, T. / ...Authors: Zhou, T. / Zhu, J. / Wu, X. / Moquin, S. / Zhang, B. / Acharya, P. / Georgiev, I.S. / Altae-Tran, H.R. / Chuang, G.Y. / Joyce, M.G. / Do Kwon, Y. / Longo, N.S. / Louder, M.K. / Luongo, T. / McKee, K. / Schramm, C.A. / Skinner, J. / Yang, Y. / Yang, Z. / Zhang, Z. / Zheng, A. / Bonsignori, M. / Haynes, B.F. / Scheid, J.F. / Nussenzweig, M.C. / Simek, M. / Burton, D.R. / Koff, W.C. / Mullikin, J.C. / Connors, M. / Shapiro, L. / Nabel, G.J. / Mascola, J.R. / Kwong, P.D.
History
DepositionJul 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3May 7, 2014Group: Other
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Jul 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_PDB_ins_code / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _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_ptnr1_PDB_ins_code / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: ENVELOPE GLYCOPROTEIN GP120 WITH LOOP D AND V5 FROM STRAIN 3415_V1_C1
H: HEAVY CHAIN OF ANTIBODY VRC-CH31
L: LIGHT CHAIN OF ANTIBODY VRC-CH31 WITH N70D MUTATION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,45025
Polymers87,6083
Non-polymers2,84122
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10230 Å2
ΔGint-92 kcal/mol
Surface area34930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.514, 67.621, 221.088
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody HEAVY CHAIN OF ANTIBODY VRC-CH31


Mass: 25571.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#3: Antibody LIGHT CHAIN OF ANTIBODY VRC-CH31 WITH N70D MUTATION


Mass: 22854.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 10 molecules G

#1: Protein ENVELOPE GLYCOPROTEIN GP120 WITH LOOP D AND V5 FROM STRAIN 3415_V1_C1


Mass: 39182.434 Da / Num. of mol.: 1 / Mutation: N70D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: 93TH057 / Gene: env / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q0ED31*PLUS
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
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 , 5 types, 395 molecules

#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#6: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 0.1M Tris, 8.25% PEG 8000, 0.02 M CdCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 18, 2011
RadiationMonochromator: APS 22ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 47596 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 39.25 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 7.6
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.522 / % possible all: 87.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→49.38 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.63 / σ(F): 1.35 / Phase error: 23.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 2409 5.07 %
Rwork0.192 --
obs0.194 47511 98.4 %
all-48269 -
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.72 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 59.43 Å2
Baniso -1Baniso -2Baniso -3
1-9.7107 Å2-0 Å2-0 Å2
2---5.5523 Å2-0 Å2
3----4.1584 Å2
Refinement stepCycle: LAST / Resolution: 2.25→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5983 0 144 382 6509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086307
X-RAY DIFFRACTIONf_angle_d0.8638557
X-RAY DIFFRACTIONf_dihedral_angle_d13.2692299
X-RAY DIFFRACTIONf_chiral_restr0.052973
X-RAY DIFFRACTIONf_plane_restr0.0031083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2505-2.29650.3111110.26052282X-RAY DIFFRACTION86
2.2965-2.34640.28551390.24742472X-RAY DIFFRACTION94
2.3464-2.4010.30941610.24132580X-RAY DIFFRACTION98
2.401-2.4610.3161290.25192613X-RAY DIFFRACTION98
2.461-2.52750.28631550.22912626X-RAY DIFFRACTION99
2.5275-2.60190.29811470.22612663X-RAY DIFFRACTION100
2.6019-2.68590.29471420.22322644X-RAY DIFFRACTION100
2.6859-2.78190.26651480.21072679X-RAY DIFFRACTION100
2.7819-2.89330.23851160.21082692X-RAY DIFFRACTION100
2.8933-3.02490.25321420.20042667X-RAY DIFFRACTION100
3.0249-3.18440.2691470.20112676X-RAY DIFFRACTION100
3.1844-3.38380.24531510.19882703X-RAY DIFFRACTION100
3.3838-3.6450.19941490.19232681X-RAY DIFFRACTION100
3.645-4.01170.20641350.16282706X-RAY DIFFRACTION100
4.0117-4.59180.17551370.14832742X-RAY DIFFRACTION100
4.5918-5.78380.17941430.16262782X-RAY DIFFRACTION100
5.7838-49.38880.21121570.20132894X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.37320.1771-0.68561.6835-0.00911.9767-0.02520.0727-0.133-0.1064-0.0845-0.15050.08730.07740.07720.12970.0093-0.04840.22890.02620.324413.6309-1.279148.099
21.8104-0.4155-0.58011.5139-0.21082.4410.0629-0.00330.20780.0187-0.0964-0.4247-0.3390.3227-0.04760.1593-0.0341-0.03540.21180.02630.356115.902621.447450.4728
32.0381-1.43070.80132.3341-0.80691.97780.10830.16130.0076-0.7149-0.21250.0655-0.0235-0.17720.06940.40190.0516-0.04480.2291-0.03070.1975-1.254927.234328.3522
43.31020.1810.94952.52170.99052.8409-0.20750.3355-0.1519-0.23560.17390.3820.2805-0.17580.00090.7835-0.066-0.14240.34440.07070.417-17.570642.08490.7513
50.07-0.1384-0.19580.64880.16930.67420.21150.2933-0.0346-0.7277-0.26060.04590.24980.1816-0.26411.12730.44550.07190.5471-0.02330.22528.853117.11879.8956
62.0992-0.52280.23494.32670.00662.03550.09590.54860.2419-0.12370.0013-0.38940.3190.1953-0.09850.80510.0448-0.09120.4650.0990.365-3.927345.6784-7.1408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN G AND (RESID 44:252 OR RESID 474:492 ) )
2X-RAY DIFFRACTION2(CHAIN G AND RESID 253:473 )
3X-RAY DIFFRACTION3(CHAIN H AND RESID 1:118 )
4X-RAY DIFFRACTION4(CHAIN H AND RESID 119:215 )
5X-RAY DIFFRACTION5(CHAIN L AND RESID 1:108 )
6X-RAY DIFFRACTION6(CHAIN L AND RESID 109:212 )

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